Microbial and human cell-free DNA biomarkers for diagnosing and assessing the severity of inflammatory bowel disease

Abstract

Disclosed herein in some embodiments are methods, compositions, and systems for distinguishing between ulcerative colitis (UC), Crohn's disease (CD) and other Inflammatory Bowel Disorders (IBD) by sequencing cell free nucleic acids. In some embodiments, microbial cell-free nucleic acid sequencing can provide data that can determine whether UC, CD, or other IBD are asymptomatic, in remission, or active. In some embodiments, microbial cell-free nucleic acid sequencing can provide data that can determine whether an active form of UC, CD, or other IBD is mild, moderate, or severe.

Description

MICROBIAL AND HUMAN CELL-FREE DNA BIOMARKERS FOR DIAGNOSINGAND ASSESSING THE SEVERITY OF INFLAMMATORY BOWEL DISEASECROSS REFERENCE

[0001] This application claims the benefit of U.S. Provisional Application No. 63 / 625,258 filed on January 25, 2024, the entirety of which is hereby incorporated by reference herein.BACKGROUND OF THE INVENTION

[0002] Massively parallel sequencing (MPS), as the name implies, is a high-throughput technology that can generate an enormous amount of information about the genetic makeup of an organism. MPS is particularly useful for genomic studies that analyze sequences across a genome such as whole genome sequencing. MPS can be used to study cell-associated DNA, as well as cell- free DNA shed into a variety of samples including blood. MPS can also be used for metagenomic sequencing applications that detect microbial genomes in a sample.

[0003] The two main subtypes of inflammatory bowel disease (IBD) are ulcerative colitis (UC) and Crohn’s disease (CD). Although the two diseases share common features, including some overlap in symptoms, the treatment plan for these subtypes can differ. An adequate treatment plan also benefits from knowledge of the severity of the disease. Nonetheless, accurate diagnosis of inflammatory diseases such as inflammatory bowel disease (IBD) and categorization of their severity remains a challenge, especially when pursued in a non-invasive manner. There is a clinical need to develop effective minimally-invasive diagnostics to accurately assess disease subtype and severity across types of inflammatory diseases including ulcerative colitis and Crohn’s disease. Provided herein are novel approaches for identifying a subtype of IBD, identifying severity of a subtype of IBD, and preparing samples useful for detecting IBD.SUMMARY OF THE INVENTION

[0004] This Summary introduces a selection of concepts that are described further below in the Detailed Description. This Summary is not intended to limit the scope of the claimed subject matter.

[0005] Disclosed herein are methods, systems, and compositions for detecting a subtype of inflammatory bowel disease (IBD) in a subject. In some embodiments, a method disclosed herein comprises: providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises subject cell-free nucleic acids (subject cfNA), microbial cell- free nucleic acids (mcfNA), or a mixture thereof; performing a sequencing assay on the cfNA to obtain sequence data; applying a classifier to the sequence data, wherein the classifier can detectat least one subtype of IBD based on an mcfNA signature, a subject cfNA signature, or a combination thereof; and determining that the subject has a subtype of inflammatory bowel disorder based at least in part on the applying of the classifier to the sequence data. In some embodiments, the classifier can detect ulcerative colitis (UC) or Crohn’s disease (CD) in the subject. In some embodiments, the classifier can distinguish between UC and CD in the subject. In some embodiments, the classifier detects UC, detects CD, or distinguishes between UC and CD at an AUC of greater than 0.7. In some embodiments, prior to (b), the subject is determined to have IBD with an unknown subtype. In some embodiments, the subject has previously had an endoscopy procedure. In some embodiments, the endoscopy procedure indicated that the subject had indeterminate colitis. In some embodiments, the classifier can detect at least one subtype of IBD based on an mcfNA signature and wherein the sequence data comprises data from mcfNA in the sample. In some embodiments, the classifier can detect at least one subtype of IBD based on an mcfNA signature and on a subject cfNA signature and wherein the sequence data comprises data from mcfNA in the sample and the subject cfNA in the sample.

[0006] Disclosed herein are methods and compositions for detecting a severity of inflammatory bowel disease (IBD) in a subject. In some embodiments, a method disclosed herein comprises: providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprise subject cell-free nucleic acids (subject cfNA), microbial cell-free nucleic acids (mcfNA), or a mixture thereof; performing a sequencing assay on the cfNA to obtain sequence data; applying a classifier to the sequence data, wherein the classifier can detect any of the following categories of severity: mild disease, moderate disease, severe disease, remission, or combination thereof; and categorizing severity of disease in the subject based at least in part on the applying of the classifier to the sequence data. In some embodiments, the categorizing in (d) comprises determining that the subject is in remission. In some embodiments, the categorizing in (d) comprises determining that the subject has mild, moderate, or severe IBD. In some embodiments, the categorizing in (d) further comprises detecting a level of severity of a subtype of IBD. In some embodiments, the subtype of IBD is ulcerative colitis (UC) or Crohn’s disease (CD).

[0007] Disclosed herein are methods and compositions for preparing a cell-free nucleic acid (cfNA) fraction from a subject with an inflammatory bowel disease (IBD) of unknown subtype. In some embodiments, a method disclosed herein comprises: providing an initial sample from the subject with the IBD of unknown subtype, the initial sample comprising cfNA comprising subject cell-free nucleic acids (subject cfNA), microbial cell-free nucleic acids (mcfNA), or a mixture thereof and wherein the cfNA comprises double-stranded cfNA, single-stranded cfNA, degradeddouble-stranded cfNA (degraded dscfNA) and degraded single-stranded cfNA (degraded sscfNA); denaturing the double-stranded cfNA and degraded dscfNA into single-stranded fragments such that the cfNA comprises: (i) the single-stranded cfNA and the degraded sscfNA originally in the initial sample; and (ii) single-stranded cfNA fragments and degraded sscfNA fragments produced by the denaturing of the double-stranded cfNA; preparing a cfNA library comprising cfNA produced in (b); and analyzing a genetic locus within the single-stranded cfNA fragments, wherein the genetic locus is located within the mcfNA, the subject cfNA, or both. In some embodiments, the cfNA comprise cfNA fragments at least 20 bases in length. In some embodiments, the cfNA comprises cfNA fragments less than 200 bases in length. In some embodiments, the cfNA comprises cfNA fragments less than 100 bases in length. In some embodiments, the genetic locus is located within the mcfNA. In some embodiments, the genetic locus is located within singlestranded cfNA or degraded sscfNA in the initial sample. In some embodiments, the genetic locus is located within double-stranded cfNA or degraded dscfNA in the initial sample. In some embodiments, the preparing a cfNA library comprises attaching 5’ adapters, 3’ adapters, or both 5’ and 3’ adapters to the cfNA. In some embodiments, the attaching 5’ adapters, 3’ adapters, or both 5’ and 3’ adapters to the cfNA occurs in the initial sample wherein the initial sample has not been subjected to an extraction assay.

[0008] Disclosed herein are methods and compositions for preparing a cell-free nucleic acids fraction from a subject with an inflammatory bowel disease (IBD). In some embodiments, a method disclosed herein comprises: providing a sample from the subject with the IBD, the sample comprising: cell -free nucleic acids (cfNA), wherein the cfNA comprise subject cell-free nucleic acids (subject cfNA), microbial cell-free nucleic acids (mcfNA), or a mixture thereof; physically enriching the sample for subject cfNA, mcfNA fragments, or both, that are less than a cutoff value between 70-200 bases to produce a size-enriched fraction of cfNA; and analyzing a genetic locus in the size-enriched fraction of cfNA, wherein the genetic locus is located within the mcfNA, the subject cfNA, or both. In some embodiments, the genetic locus comprises a plurality of genetic loci that constitute a signature that distinguishes between ulcerative colitis (UC) and Crohn’s disease (CD). In some embodiments, the cutoff value is less than about 90 bases. In some embodiments, the methods disclosed herein further comprise physically enriching the sample for subject cfNA and mcfNA greater than about 10 bases in length. In some embodiments, the genetic locus analyzed in the size-enriched fraction of cfNA is located within the mcfNA. In some embodiments, the physically enriching comprises directly physically enriching the sample or indirectly physically enriching the sample. In some embodiments, the directly physically enriching comprises subjecting the cfNA to a size selection device. In some embodiments, the size selectiondevice comprises beads or a gel electrophoresis device. In some embodiments, the indirectly physically enriching results from a process that does not involve use of sharp cutoff values for size selection. In some embodiments, the methods disclosed herein comprise screening the subject for IBD prior to, simultaneously, or following the providing the sample from the subject in (a). In some embodiments, the methods disclosed herein comprise performing an endoscopic procedure on the subject that identifies the subject as having indeterminate colitis or obtaining results from an endoscopic procedure performed on the subject, wherein the endoscopic procedure indicated the subject has indeterminate colitis. In some embodiments, the endoscopy is performed prior to, simultaneously, or following the providing the sample from the subject in (a). In some embodiments, the physically enriching comprises enriching the sample for degraded cfNA.

[0009] Disclosed herein are methods and compositions for treating a subject diagnosed as having a subtype of Inflammatory Bowel Disease (IBD). In some embodiments, the methods disclosed herein comprise: treating the subject for the subtype of IBD by administering a medicament for the subtype of IBD to the subject, wherein the diagnosis is based at least in part on a method comprising: providing a sample from the subject, wherein the subject has an unknown subtype of inflammatory bowel disease (IBD), the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises a mixture of subject cell-free nucleic acids (subject cfNA) and microbial cell- free nucleic acids (mcfNA); performing a sequencing assay on the cfNA to obtain sequence data; applying a classifier to the sequence data, wherein the classifier can detect at least one subtype of IBD based on a mcfNA signature, a subject cfNA signature, or a combination thereof; and determining that the subject has a subtype of inflammatory bowel disorder based at least in part on the applying of the classifier to the sequence data.

[0010] Disclosed herein are methods and compositions for treating a subject diagnosed as having a subtype of Inflammatory Bowel Disease (IBD) categorized as severe, moderate, mild, or in remission. In some embodiments, the methods disclosed herein comprise: treating the subject for the subtype of IBD by administering a medicament for the subtype of IBD to the subject at a dose consistent with the severity of IBD, wherein the diagnosis is based at least in part on a method comprising: providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises a mixture of subject cell-free nucleic acids (subject cfNA) and microbial cell-free nucleic acids (mcfNA); performing a sequencing assay on the cfNA to obtain sequence data; applying a classifier to the sequence data, wherein the classifier can categorize severity of a subtype of IBD based on a mcfNA signature, a subject cfNA signature, or a combination thereof; and categorizing the severity of the subtype of IBD in the subject as severe,moderate, mild, or in remission, based at least in part on the applying of the classifier to the sequence data.

[0011] Disclosed herein are methods and compositions for treating and monitoring a subject diagnosed as having an Inflammatory Bowel Disease (IBD) subtype in remission. In some embodiments, the methods disclosed herein comprise: treating the subject for the IBD subtype in remission by administering a first medicament to the subject at an initial maintenance dose; between 2 weeks to 6 months after (a), providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises a mixture of subject cell-free nucleic acids (subject cfNA) and microbial cell-free nucleic acids (mcfNA); performing a sequencing assay on the mixture of mcfNA and subject cfNA to obtain sequence data; applying a classifier to the sequence data, wherein the classifier can categorize a subtype of IBD as being severe, moderate, mild, or in remission, based on a mcfNA signature, a subject cfNA signature, or a combination thereof; categorizing the subtype of IBD as severe, moderate, mild or in remission, based at least in part on the applying of the classifier to the sequence data; and if the subtype of IBD is categorized as in remission, continuing to treat the subject with the first medicament at the initial maintenance dose, reducing the dose of the first medicament, or discontinuing use of the first medicament; and if the subtype of IBD is categorized as mild, moderate or severe, treating the subject by: increasing the dose of the first medicament to a dose higher than the first initial maintenance dose; administering a second medicament to the subject in addition to, or in place of, the first medicament; performing an endoscopic procedure on the subject in order to detect the severity of the subtype of IBD and identify the location of the subtype of IBD; or performing a surgery on the subject in order to remove a portion of the digestive tract of the subject if the endoscopic procedure confirms that the subject is suffering from a moderate or severe subtype of IBD.

[0012] Disclosed herein are methods and compositions for treating and monitoring a subject diagnosed as having an Inflammatory Bowel Disease (IBD) subtype. In some embodiments, the methods disclosed herein comprise: treating the subject for the IBD subtype by administering a first medicament to the subject at an initial induction dose; about 2 to 6 weeks after (a), providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises a mixture of subject cell-free nucleic acids (subject cfNA) and microbial cell-free nucleic acids (mcfNA); performing a sequencing assay on the mixture of mcfNA and subject cfNA to obtain sequence data; applying a classifier to the sequence data, wherein the classifier can categorize a subtype of IBD as being severe, moderate, mild, or in remission, based on a mcfNA signature, a subject cfNA signature, or a combination thereof; categorizing the subtype of IBD assevere, moderate, mild or in remission, based at least in part on the applying of the classifier to the sequence data; and if the subtype of IBD is categorized as in remission, continuing to treat the subject with the first medicament at the initial maintenance dose, reducing the dose of the first medicament, or discontinuing use of the first medicament; and if the subtype of IBD is categorized as mild, moderate or severe, and indicates the subject is not responding to the first medicament, treating the subject by: increasing the dose of the first medicament to a dose higher than the first initial maintenance dose; administering a second medicament to the subject in addition to, or in place of, the first medicament; performing an endoscopic procedure on the subject in order to detect the severity of the subtype of IBD and identify the location of the subtype of IBD; or performing a surgery on the subject in order to remove a portion of the digestive tract of the subject if the endoscopic procedure confirms that the subject is suffering from a moderate or severe subtype of IBD.

[0013] Disclosed herein are methods and compositions for treating and monitoring a subject wherein the subject has received a surgical intervention for an Inflammatory Bowel Disease (IBD) subtype. In some embodiments, the methods disclosed herein comprise: at least 2-6 weeks following the surgical intervention, providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises a mixture of subject cell-free nucleic acids (subject cfNA) and microbial cell-free nucleic acids (mcfNA);performing a sequencing assay on the mixture of mcfNA and subject cfNA to obtain sequence data; applying a classifier to the sequence data, wherein the classifier can categorize a subtype of IBD as being severe, moderate, mild, or in remission, based on a mcfNA signature, a subject cfNA signature, or a combination thereof; categorizing the subtype of IBD as severe, moderate, mild or in remission, based at least in part on the applying of the classifier to the sequence data; and if the subtype of IBD is categorized as in remission, administer, or continue to administer, a maintenance therapy; and if the subtype of IBD is categorized as mild, moderate or severe, treating the subject by: adjusting the subject’s treatment regimen by adding or subtracting a medication or changing a dose of a medication; performing an endoscopic procedure on the subject in order to detect the severity or location of the subtype of IBD and identify the location of the subtype of IBD; or performing another surgery on the subject in order to remove a portion of the digestive tract of the subject if the endoscopic procedure confirms that the subject is suffering from a moderate or severe subtype of IBD. In some embodiments, an endoscopic procedure performed prior to (a) has indicated the subject has indeterminate colitis. In some embodiments, the IBD is considered to be indeterminate because of inaccessible regions of the bowel or because of indeterminate disease manifestation. In some embodiments, the indeterminate disease manifestation is due to a finding of continuousinflammatory patches that could be consistent with CD or UC. In some embodiments, the classifier can detect ulcerative colitis (UC) or Crohn’s disease (CD). In some embodiments, the classifier can distinguish between UC and CD. In some embodiments, the maintenance therapy comprises an anti-inflammatory drug or corti co- steroid. In some embodiments, the at least two types of IBD comprise disease that is mild, moderate, severe, or in remission, or any combination thereof. In some embodiments, if the subject is determined to be in remission, further comprising administering a maintenance treatment to the subject. In some embodiments, if the subject is determined to have mild, moderate, or severe disease, administering a drug for mild, moderate, or severe disease. In some embodiments, if a subject is determined to have a mild, moderate, or severe subtype of IBD, and the subject is receiving a drug regimen, further comprising adjusting or changing the drug regimen. In some embodiments, if the subject is determined to have mild, moderate, or severe disease, performing an endoscopy on the subject in order to identify regions of inflammation. In some embodiments, if the subject is determined to have mild, moderate, or severe disease, the methods disclosed herein further comprise performing surgery on the patient to remove all of, or a portion of, the anus, rectum, large intestine, small intestine, digestive tract, or any combination thereof. In some embodiments, the screening of the subject comprises detection of a lesion, ulceration, inflammation, bleeding pattern, or disease location in the gastrointestinal tract. In some embodiments, the subject has an indeterminate endoscopic biopsy prior to the providing the sample in (a). In some embodiments, the subject has had an indeterminate biopsy that detected continuous inflammatory regions or lesions along a section of the gastrointestinal tract. In some embodiments, the subject has had an endoscopic procedure of the gastrointestinal tract that results in a finding of IBD, UC, CD, or combination thereof. In some embodiments, the method is performed in order to confirm the finding of IBD, UC, CD, or combination thereof. In some embodiments, the methods disclosed herein further comprise performing an endoscopic procedure on the gastrointestinal tract of the subject if UC, CD, mild disease, moderate disease, or severe disease is detected by the method.

[0014] Disclosed herein are methods and compositions for guiding an endoscopic procedure. In some embodiments, the methods disclosed herein comprise collecting a sample from a patient with an inflammatory bowel disease (IBD) of unknown subtype, wherein: the sample comprises cell- free nucleic acids (cfNA) comprising human cell-free nucleic acids (human cfNA), microbial cell- free nucleic acids (mcfNA), or a mixture thereof; the patient is planning to undergo an endoscopy procedure; and the sites to be biopsied by the endoscopy procedure have not yet been determined; performing a sequencing assay on the cfNA to obtain sequence data; applying a classifier to the sequence data, wherein the classifier can distinguish between at least two types of inflammatorybowel disorder (IBD) based on a mcfNA signature, a subject cfNA signature, or a combination thereof; and determining that the subject has a first type of IBD based at least in part on the applying of the classifier to the sequence data, wherein: the first type of IBD is associated with inflammatory regions along the entirety of the digestive tract and, the second type of IBD is associated with inflammatory regions localized to the large intestine, the rectum, or both the large intestine and the rectum; and wherein if the first type of IBD is detected, an endoscopic procedure is performed that targets multiple locations along the entirety of the digestive tract; and if the second type of IBD is detected, an endoscopic procedure is performed that targets a region limited to the large intestine and the rectum. In some embodiments, the first type of IBD is Crohn’s disease (CD). In some embodiments, the second type of IBD is ulcerative colitis (UC). In some embodiments, the targeting of multiple locations along the entirety of the digestive tract comprises performing the endoscopic procedure on an ilium, a large bowel, or both. In some embodiments, the at least two types of IBD comprise at least two of: mild IBD, moderate IBD, severe IBD, or IBD in remission. In some embodiments, the methods disclosed herein further comprise screening the subject for IBD. In some embodiments, the screening comprises a physical examination, blood test, stool test, imaging study, reported symptoms, medications, personal medical history, family medical history, or any combination thereof. In some embodiments, the screening comprises a clinical evaluation based on one or more features selected from the group consisting of: abdominal pain, rectal bleeding, weight loss, fatigue, personal medical history, family medical history, lifestyle, or any combination thereof. In some embodiments, the screening is inconclusive for IBD, subtype of IBD, or severity of subtype of IBD. In some embodiments, the methods disclosed herein further comprise physically enriching the sample for human and microbial cell-free nucleic acid fragments that are less than a cutoff value between 70-200 bases. In some embodiments, the physically enriching comprises producing a size-enriched fraction of the cfNA by: binding the cfNA to a solid support capable of separating the cfNA based on size and eluting the cfNA from the solid support to obtain size-selected cfNA; subjecting the cfNA to a size-selection electrophoresis; or a combination of (a) and (b). In some embodiments, the method further comprises analyzing a genetic locus in the size-enriched fraction of cfNA. In some embodiments, the analyzing the genetic locus in the size-enriched fraction of cfNA comprises sequencing the size-enriched fraction of cfNA to obtain sequence reads. In some embodiments, the analyzing or determining the genetic locus comprises determining a ratio of a number of sequence reads covering the genetic locus to the number of reads covering a flanking region. In some embodiments, the number of sequence reads covering the first genomic region comprises the number of sequence reads within 500 bp of the genetic locus, and wherein the number of sequencereads covering the flanking region comprises a number of sequence reads located more than 5OObp from the genetic locus but within 2000 bp in either a 5’ or 3’ direction from the genetic locus. In some embodiments, the ratio comprises a natural log of the number of sequence reads covering the first genomic region divided by the number of sequence reads covering the flanking region. In some embodiments, the ratio comprises a peak-to-flank ratio or a trough-to-flank ratio of sequence reads. In some embodiments, the methods disclosed herein further comprise determining that a gene is differentially enriched when the value of the ratio for the gene is 0.3 or greater. In some embodiments, the sample comprises a biological fluid. In some embodiments, the method further comprises analyzing a genetic locus in the mcfNA or the subject cfNA, or a combination thereof. In some embodiments, the methods disclosed herein further comprise analyzing a genetic locus within a human genome. In some embodiments, the genetic locus is within microbial cell-free DNA derived from a Propionibactierum, a Lactococcus, Haemophilus, an Escherichia, Rothia, a Malassezia, a Streptococcus, a Rothia, an Actinomyces, a Klebsiella, a Dermacoccus, an Acinetobacter, a Lactobacillus, or any combination thereof. In some embodiments, the genetic locus is within microbial cell-free DNA derived from Acinetobacter, Staphylococcus, Blautia, Anoxybacillus, Paracoccus, or any combination thereof. In some embodiments, the analyzing comprises performing high throughput sequencing on the sample. In some embodiments, the biological fluid is a non-fecal biological fluid. In some embodiments, the sample comprises blood, serum, plasma, cerebrospinal fluid, fluid from lavage, fluid from bronchoalveolar lavage, synovial fluid, or urine. In some embodiments, the sample is a plasma sample. In some embodiments, the sample comprises cfNA derived from or purified from a biological fluid. In some embodiments, the subject with an inflammatory bowel disorder has symptoms consistent with both ulcerative colitis and Crohn’s Disease. In some embodiments, the symptoms comprise: long-term inflammation of the digestive tract, digestive discomfort, stomach cramps and pain, diarrhea, constipation, urgent need to have a bowel movement, feeling as though a bowel movement was incomplete, rectal bleeding, loss of appetite, weight loss, fatigue, night sweats, irregular periods, or any combination thereof. In some embodiments, the subject is human. In some embodiments, the methods disclosed herein further comprise administering a medicament to the subject. In some embodiments, the methods disclosed herein further comprise distinguishing between a first, a second and a third type of inflammatory bowel disease or disorder. In some embodiments, the analyzing comprises analyzing data generated from sequence reads obtained from both the human and mcfNA. In some embodiments, the first type of inflammatory bowel disease or disorder comprises ulcerative colitis and the second type of inflammatory bowel disease or disorder is Crohn’s Disease. In some embodiments, the first type of inflammatory bowel disease or disordercomprises a severe inflammatory bowel disease or disorder and the second type of inflammatory bowel disease or disorder comprises a moderate inflammatory bowel disease. In some embodiments, the methods disclosed herein further comprise distinguishing between a first, a second and a third type of inflammatory bowel disease or disorder. In some embodiments, the third type of inflammatory bowel disease or disorder comprises a mild inflammatory bowel disease or disorder. In some embodiments, the method further comprises determining that the inflammatory bowel disorder comprises Crohn’s disease. In some embodiments, the method further comprises determining that the inflammatory bowel disorder comprises ulcerative colitis. In some embodiments, the analyzing the sequence reads comprises use of machine learning. In some embodiments, the analyzing the sequence reads comprises applying one or more classifiers to sequence data. In some embodiments, the one or more classifiers are assessed using a receiver operating characteristics curve (ROC). In some embodiments, the methods disclosed herein further comprise determining a diversity of overall detected microbes from the microbial cell-free DNA, wherein the subject is determined to have an active disease when the sample from the subject has a higher alpha diversity of overall detected microbes relative to an otherwise comparable sample with a lower alpha diversity of overall detected microbes. In some embodiments, the methods disclosed herein further comprise determining the disease is severe, and wherein the determining comprises detecting a higher alpha diversity of overall detected microbes in the sample from the subject relative to an otherwise comparable sample with a lower alpha diversity of overall detected microbes. In some embodiments, the methods disclosed herein further comprise determining the disease comprises ulcerative colitis, wherein the determining comprises analyzing the sequence reads to detect in the sample a presence of cell-free DNA derived from a Propionibactierum, a Lactococcus, Haemophilus, an Escherichia, Rothia, a Malassezia, Streptococcus, Rothia, a Malassezia, an Actinomyces, a Klebsiella, a Dermacoccus, an Acinetobacter, a Lactobacillus, or any combination thereof. In some embodiments, the methods disclosed herein further comprise determining the disease comprises ulcerative colitis, wherein the determining comprises analyzing the sequence reads to detect in the sample a presence of cell-free DNA derived from an Afipia, a Bifidobacterium, a Brochothrix, a Companilactobacillus, a Coprobacillus, an Escherichia, a Leptospira, a Methylobacterium, a Pantoea, a Parasutterella, a Pichia, a Proteus, a Sphingobacterium, an Achromobacter, an Acinetobacter, an Actinomyces, an Aeribacillus, an Alishewanella, an Alistipes, an Alphacoronavirus, an Alphainfluenzavirus, an Anoxybacillus, an Aureobasidium, a Bacillus, a Betacoronavirus, a Blautia, a Burkholderia, a Caldibacillus, a Caldicellulosiruptor, a Campylobacter, a Capnocytophaga, a Chryseobacterium, a Citrobacter, a Clostridia UnClass UnClass UnClass, a Clostridium, a Collinsella, a Coprococcus, aCupriavidus, a Cyberlindnera, a Delftia, a Dependoparvovirus, a Dialister, a Duffyella, an Emesvirus, an Enhydrobacter, an Enterobacter, an Eubacteriales Family XIII. Incertae Sedis UnClass, an Eubacteriales UnClass UnClass, an Eubacterium, a Finegoldia, a Francisella, a Geobacillus, an Inovirus, an Intestinibacter, a Kingella, a Klebsiella, a Kocuria, a Lachnoanaerobaculum, a Lachnoclostridium, a Lentivirus, a Leuconostoc, a Mediterraneibacter, a Megasphaera, a Melampsora, a Mesorhizobium, a Methanococcus, a Methanosarcina, a Methanothrix, a Methylorubrum, a Moraxella, a Mycobacterium, a Mycolicibacterium, a Nesterenkonia, an Orthopoxvirus, a Paenibacillus, a Paenirhodobacter, a Paraburkholderia, a Paracoccus, a Pelomonas, a Prevotella, a Pseudomonas, aRalstonia, a Rhodococcus, aRothia, a Ruminococcus, a Saccharomyces, a Schaalia, a Selenomonas, a Sphingobium, a Sphingomonas, a Staphylococcus, a Stenotrophomonas, a Stomatobaculum, a Stutzerimonas, a Sulfurihydrogenibium, a Sutterella, a Tepidimonas, a Tepidiphilus, a Teseptimavirus, a Thermicanus, a Thermoanaerobacterium, a Thomasclavelia, a Trichuris, a Tyzzerella, a Variovorax, a Veillonella, a Weizmannia, a Williamsia, an Enterococcus, an Alicyclobacillus, a Bacteria UnClass UnClass UnClass UnClass UnClass, a Bradyrhizobium, a Brucella, a Curvibacter, a Dermacoccus, an Elaeophora, a Faecalibacterium, a Flavonifr actor, a Halomonas, a Lachnospira, a Lacticaseibacillus, a Lambdavirus, a Liquorilactobacillus, a Lymphocryptovirus, a Novosphingobium, a Rhizopus, a Rhodopseudomonas, a Roseburia, a Schizo saccharomyces, a Streptomyces, a Tequatrovirus, a Vedamuthuvirus, a Fervidobacterium, a Microbacterium, a Retroviridae UnClass, a Neurospora, a Pseudacidovorax, or any combination thereof. In some embodiments, the methods disclosed herein further comprise determining the disease comprises Crohn’s disease, wherein the determining comprises analyzing the sequence reads to detect in the sample a presence of cell-free DNA derived from Propionibactierum, Lactococcus, Haemophilus, Escherichia, Rothia, Malassezia, Streptococcus, Actinomyces, Klebsiella, Dermacoccus, Acinetobacter, Lactobacillus, or any combination thereof. In some embodiments, the methods disclosed herein further comprise determining the disease is Crohn’s disease, wherein the determining comprises analyzing the sequence reads to detect in the sample a presence of cell-free DNA derived from an Afipia, a Bifidobacterium, a Brochothrix, a Companilactobacillus, a Coprobacillus, an Escherichia, a Leptospira, a Methylobacterium, a Pantoea, a Parasutterella, a Pichia, a Proteus, a Sphingobacterium, an Achromobacter, an Acinetobacter, an Actinomyces, an Aeribacillus, an Alishewanella, an Alistipes, an Alphacoronavirus, an Alphainfluenzavirus, an Anoxybacillus, an Aureobasidium, a Bacillus, a Betacoronavirus, a Blautia, a Burkholderia, a Caldibacillus, a Caldicellulosiruptor, a Campylobacter, a Capnocytophaga, a Chryseobacterium, a Citrobacter, aClostridia UnClass UnClass UnClass, a Clostridium, a Collinsella, a Coprococcus, a Cupriavidus, a Cyberlindnera, a Delftia, a Dependoparvovirus, a Dialister, a Duffyella, an Emesvirus, an Enhydrobacter, an Enterobacter, an Eubacteriales Family XIII. Incertae Sedis UnClass, an Eubacteriales UnClass UnClass, an Eubacterium, a Finegoldia, a Francisella, a Geobacillus, an Inovirus, an Intestinibacter, a Kingella, a Klebsiella, a Kocuria, a Lachnoanaerobaculum, a Lachnoclostridium, a Lentivirus, a Leuconostoc, a Mediterraneibacter, a Megasphaera, a Melampsora, a Mesorhizobium, a Methanococcus, a Methanosarcina, a Methanothrix, a Methylorubrum, a Moraxella, a Mycobacterium, a Mycolicibacterium, a Nesterenkonia, an Orthopoxvirus, a Paenibacillus, a Paenirhodobacter, a Paraburkholderia, a Paracoccus, a Pelomonas, a Prevotella, a Pseudomonas, aRalstonia, a Rhodococcus, aRothia, a Ruminococcus, a Saccharomyces, a Schaalia, a Selenomonas, a Sphingobium, a Sphingomonas, a Staphylococcus, a Stenotrophomonas, a Stomatobaculum, a Stutzerimonas, a Sulfurihydrogenibium, a Sutterella, a Tepidimonas, a Tepidiphilus, a Teseptimavirus, a Thermicanus, a Thermoanaerobacterium, a Thomasclavelia, a Trichuris, a Tyzzerella, a Variovorax, a Veillonella, a Weizmannia, a Williamsia, an Enterococcus, an Alicyclobacillus, a Bacteria UnClass UnClass UnClass UnClass UnClass, a Bradyrhizobium, a Brucella, a Curvibacter, a Dermacoccus, an Elaeophora, a Faecalibacterium, a Flavonifr actor, a Halomonas, a Lachnospira, a Lacticaseibacillus, a Lambdavirus, a Liquorilactobacillus, a Lymphocryptovirus, a Novosphingobium, a Rhizopus, a Rhodopseudomonas, a Roseburia, a Schizo saccharomyces, a Streptomyces, a Tequatrovirus, a Vedamuthuvirus, a Fervidobacterium, a Microbacterium, a Retroviridae UnClass, a Neurospora, a Pseudacidovorax, or any combination thereof. In some embodiments, the methods disclosed herein further comprise determining the disease comprises mild, moderate, or severe ulcerative colitis, wherein the determining comprises analyzing the sequence reads to detect an elevated or decreased level of cell-free DNA in the sample derived from Acinetobacter, Staphylococcus, Blautia, Anoxybacillus, Paracoccus, or any combination thereof, relative to an otherwise comparable sample from a subject that is asymptomatic or in remission for ulcerative colitis. In some embodiments, the methods disclosed herein further comprise determining the disease comprises mild, moderate, or severe ulcerative colitis, wherein the determining comprises analyzing the sequence reads to detect an elevated or decreased level of cell-free DNA in the sample derived from an Uroviricota, a Chromadorea, a Clostridia, a Coriobacteriia, a Sordariomycetes, a Eubacteriales, a Propionibacteriales, a Sordariales, an Alicyclobacillaceae, a Bacteroidaceae, a Burkholderiales UnClass, a Caudoviricetes UnClass UnClass, a Clostridiaceae, an Eubacteriales UnClass, a Lachnospiraceae, a Micrococcaceae, an Onchocercidae, anOscillospiraceae, a Phyllobacteriaceae, a Propionibacteriaceae, a Sordariaceae, a Streptococcaceae, a Sutter ellaceae, an Alicyclobacillus, a Bacillus, a Blautia, a Caldibacillus, a Ceduovirus, a Clostridium, a Collinsella, a Coprococcus, a Delftia, a Dorea, an Enterocloster, an Eubacteriales UnClass UnClass, a Faecalibacterium, a Flavonifr actor, a Kocuria, a Lachnospira, a Lachnospiraceae UnClass, a Lambdavirus, aMediterraneibacter, a Micrococcus, a Moineauvirus, a Neurospora, a Novosphingobium, aRoseburia, a Ruminococcus, a Skunavirus, a Sphingobium, a Tepidimonas, a Tyzzerella, an Acinetobacter or any combination thereof, relative to an otherwise comparable sample from a subject that is asymptomatic or in remission for ulcerative colitis. In some embodiments, the methods disclosed herein further comprise determining the disease comprises mild, moderate, or severe Crohn’s disease, wherein the determining comprises analyzing the sequence reads to detect an elevated presence of cell-free DNA in the sample derived from Malassezia, Acinetobacter, Streptococcus, Lactobacillus, Lactobacillus, or any combination thereof, relative to an otherwise comparable sample from a subject that is asymptomatic or in remission for Crohn’s disease. In some embodiments, the methods disclosed herein further comprise determining the disease comprises mild, moderate, or severe Crohn’s disease, wherein the determining comprises analyzing the sequence reads to detect an elevated presence of cell-free DNA in the sample derived from Malassezia restricta, Acinetobacter baumannii, Streptococcus sanguinis. Lactobacillus plantarum, Lactobacillus crispatus, or any combination thereof, relative to an otherwise comparable sample from a subject that is asymptomatic or in remission for Crohn’s disease. In some embodiments, the methods disclosed herein further comprise determining that the subject has a disease based at least in part on the analyzing the genetic locus. In some embodiments, the determining that the subject has a disease based on the biomarkers comprises a sensitivity of AUC >0.95. In some embodiments, the sequencing comprises sequencing 100 million to 400 million paired-end reads per sample. In some embodiments, the sequencing comprises sequencing 300 million to 400 million paired-end reads per sample. In some embodiments, the sequencing comprises from 5X to 10X average coverage per base pair per sample. In some embodiments, the sequencing further comprises enriching for cell-free nucleic acids of less than 170 base pairs in length. In some embodiments, the analyzing the sequence reads comprises calculating a log2 effect size, wherein a positive number is an increase, and a negative number is a decrease. In some embodiments, the methods disclosed herein further comprise generating a DNA library from the cell-free DNA prior to the sequencing. In some embodiments, the generating the DNA library comprises attaching an adapter to one or both ends of the DNA to produce adapted DNA. In some embodiments, the medicament comprises an aminosalicylate, a mesalamine, a 5-aminosalicylic acid (5-ASA), a steroid, a prednisolone, athiopurine, a JAK inhibitor, an anti-TNF antibody, a TNF inhibitor, a ustekinumab, a tofacitinib, an infliximab, a golimumab, a vedolizumab, a mirikizumab, a a4p7 integrin, an IL- 12 cytokine, an IL-23 cytokine, a small molecule targeting sphingosine- 1 -phosphate, or any combination thereof. In some embodiments, prior to (b), the subject is determined to have IBD with an unknown subtype. In some embodiments, the subject has previously had an endoscopy procedure. In some embodiments, the endoscopy procedure indicated that the subject had indeterminate colitis. In some embodiments, the cfNA comprises cfDNA. In some embodiments, the cfNA comprises cfRNA, mRNA. In some embodiments, the cfNA comprises bacterial cfDNA, fungal cfDNA, parasitic cfDNA, viral cfDNA, or any combination thereof. In some embodiments, the cfNA is not mitochondrial DNA. In some embodiments, the method does not comprise analysis of total cfNA, total subject cfNA, total mcfNA, or any combination thereof. In some embodiments, the cfNA does not comprise fetal nucleic acids. In some embodiments, the subject is not a transplant recipient. In some embodiments, the cfNA does not comprise a mixture of donor-derived cfDNA and host-derived cfDNA. In some embodiments, the analyzing or determining the genetic locus comprises determining a ratio of a number of sequence reads covering the genetic locus to the number of reads covering a flanking region. In some embodiments, the number of sequence reads covering the first genomic region comprises the number of sequence reads within 500 bp of the genetic locus, and wherein the number of sequence reads covering the flanking region comprises a number of sequence reads located more than 500bp from the genetic locus but within 2000 bp in either a 5’ or 3’ direction from the genetic locus. In some embodiments, the ratio comprises a natural log of the number of sequence reads covering the first genomic region divided by the number of sequence reads covering the flanking region. In some embodiments, the ratio comprises a peak-to-flank ratio or a trough-to-flank ratio of sequence reads. In some embodiments, the methods disclosed herein further comprise determining that a gene is differentially enriched when the value of the ratio for the gene is 0.3 or greater. In some embodiments, the methods disclosed herein further comprise analyzing a genetic locus in the mcfNA or the subject cfNA, or a combination thereof. In some embodiments, the methods disclosed herein further comprise analyzing a genetic locus within a human genome. In some embodiments, the method comprises detecting: a relative enrichment, wherein a relative enrichment comprises a peak-to-flank ratio of at least 0.1; a relative depletion, wherein the relative depletion comprises a trough-to-flank ratio of at least 0.1; or a combination of (a) and (b). In some embodiments, the method comprises distinguishing between the subject having Crohn’s disease and being healthy based at least in part on detecting: a relative enrichment of GPIHBP1, SLC6A4, ZCWPW1, LINC00482, FENDRR, or any combination thereof; a relative depletion of C3, SNURF, SNRPN, NM_001371415, ACE2, orany combination thereof; or any combination of (a) and (b). In some embodiments, the methods disclosed herein comprise distinguishing between the subject having Ulcerative colitis and being healthy based at least in part on detecting: a relative enrichment of ACE2, C3, NM_001371415, SNURF, TMEM259, or any combination thereof; a relative depletion of LINC00482, NR2F1, FENDRR, APOH, SLC6A4, or any combination thereof; or any combination of (a) and (b). In some embodiments, the method comprises distinguishing between the subject having Ulcerative colitis and having Crohn’s disease based at least in part on detecting: a relative enrichment of HTT, PDGFA, HRAT92, MS4A10, KANK2, or any combination thereof; a relative depletion of SNORA23, AIF1, FANCF, ASF1B, TMEM259, or any combination thereof; or any combination of (a) and (b). In some embodiments, the method comprises distinguishing between the subject having mild Ulcerative colitis and having moderate Ulcerative colitis based at least in part on detecting: a relative enrichment of RHO, CASC4, KLK9, HSPA12B, NM 001371415, or any combination thereof; a relative depletion of HCN2, LINC01410, MBNL3, PUS1, LTBP3, or any combination thereof; or any combination of (a) and (b). In some embodiments, the method comprises distinguishing between the subject having mild Ulcerative colitis and being in remission for Ulcerative colitis based at least in part on detecting: a relative enrichment of MIA3, RHO, 0LIG2, MAML3, SDC2, or any combination thereof; a relative depletion of HCN2, TBX10, RUBCNL, KANK2, ARHGEF18, or any combination thereof; or any combination of (a) and (b). In some embodiments, the method comprises distinguishing between the subject having mild ulcerative colitis and having severe Ulcerative colitis based at least in part on detecting: a relative enrichment of GDPD5, FBXO27, FAM110C, GFI1B, IFI27L2, or any combination thereof; a relative depletion of NM 001371343, DNAJB8-AS1, EYS, TPSB2, TTLL10, or any combination thereof; or any combination of (a) and (b). In some embodiments, the method comprises distinguishing between the subject having moderate Ulcerative colitis and being in remission for Ulcerative colitis based at least in part on detecting: a relative enrichment of ARHGAP33, KDM1A, MYB, SDC2, RPS6KA2, or any combination thereof; a relative depletion of SIDT1, RUBCNL, DMRTB1, TMEM143, E2F3, or any combination thereof; or any combination of (a) and (b). In some embodiments, the method comprises distinguishing between the subject having moderate Ulcerative colitis and having severe Ulcerative colitis based at least in part on detecting: a relative enrichment of HPSE, ANGPTL4, HSPB2-C1 lorf52, IFI27L2, KLHL22, or any combination thereof; a relative depletion of ADAMTS14, TBX15, MY018B, NM_001371417, SLC22A18AS, or any combination thereof; or any combination of (a) and (b). In some embodiments, the method comprises distinguishing between the subject having severe Ulcerative colitis and being in remission for Ulcerative colitis based at least in part on detecting: a relativeenrichment of EX0C2, IGSF3, PTGIS, ECHS1, H0XC8, or any combination thereof; a relative depletion of DNAJB8-AS, DMRTB1, MS4A10, MY018B, C8orf74, or any combination thereof; or any combination of (a) and (b). In some embodiments, the method comprises distinguishing between the subject having mild Crohn’s disease and having moderate Crohn’s disease based at least in part on detecting a relative enrichment of POP7, FGF6, or a combination thereof. In some embodiments, the method comprises distinguishing between the subject having mild Crohn’s disease and being in remission for Crohn’s disease based at least in part on detecting a relative enrichment of ST8SIA2, TNKS1BP1, POP7, or any combination thereof. In some embodiments, the method comprises distinguishing between the subject having mild Crohn’s disease and having severe Crohn’s disease based at least in part on detecting: a relative enrichment of SMYD4, LPCAT2, AADACL3, DPYSL5, TDRP, LOC100240728, or any combination thereof; a relative depletion of SOX11, HSPB9, MIR378I, GAL3ST4, or any combination thereof; or any combination of (a) and (b). In some embodiments, the method comprises distinguishing between the subject having moderate Crohn’s disease and being in remission for Crohn’s disease based at least in part on detecting a relative enrichment of MUC12, NAA40, UBE2E2-AS1, MHENCR, UBE2E2, or any combination thereof. In some embodiments, the method comprises distinguishing between the subject having moderate Crohn’s disease and having severe Crohn’s disease based at least in part on detecting: a relative enrichment of KPTN, SHISA5, PRSS38, SLCO2A1, AMDHD2, ST8SIA2, or any combination thereof; a relative depletion of SOX11, CLEC4G, MIR378I, or any combination thereof; or any combination of (a) and (b). In some embodiments, the method comprises distinguishing between the subject having severe Crohn’s disease and being in remission for Crohn’s disease based at least in part on detecting: a relative enrichment of ST8SIA2, CLIP3, LOC101929243, AMDHD2, UBE2E2, or any combination thereof a relative depletion of GAL3ST4, CLEC4G, MIR378I, HSPB9, SOX11, or any combination thereof; or any combination of (a) and (b). Disclosed herein in some embodiments is a system configured to perform any one of the methods disclosed herein. In some embodiments, the system is configured to present a result of the analysis of the sequence reads to the healthcare provider. In some embodiments, the system is configured to provide the healthcare provider with a clinical interpretation of the result of the analysis of the sequence reads. In some embodiments, the clinical interpretation of the result of the analysis of the sequence reads comprises that the patient has ulcerative colitis, Crohn’s disease, or any other IBD syndrome or disease. In some embodiments, the system is configured to recommend to the healthcare provider an administration of a therapy for the disease.INCORPORATION BY REFERENCE

[0015] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference in their entireties to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.BRIEF DESCRIPTION OF THE DRAWINGS

[0016] The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which:

[0017] FIG. 1 shows a Pilot Study Biosample Outline.

[0018] FIG. 2A shows a density plot of MPM abundances per sample. FIG. 2B shows the frequency of microbes within a given MPM range per sample.

[0019] FIG. 3A shows the fraction of microbes detected in each sample at various down sampling on to original full sampling. FIG. 3B shows a Pearson correlation between down sampling and original sampling.

[0020] FIG. 4A shows the number of detected microbes unique to the disclosed methods versus the number of detected microbes unique to stool whole genome shotgun sequencing (WGS) versus the overlap between both. FIG. 4B shows a representative comparison of stool microbes. WGS is provided as a fraction of whole = 1.00. FIG. 4C shows samples with elevated number of microbes unique to KT are associated with severe diseases. FIG. 4D shows a ratio of number of overlapping microbes versus unique to stool.

[0021] FIG. 5A shows a number of detected microbes, specifically eukaryotes, unique to the disclosed methods versus unique to stool by ITS2 sequencing versus overlap between both. FIG. 5B shows samples with elevated number of microbes, specifically eukaryotes / fungi, unique to KT are associated with severe disease states.

[0022] FIGs. 6A-6D show the alpha diversity measurements for UC and asymptomatic patient populations. FIG. 6A and FIG. 6C show a species level assessment of unique detected microbes and Simpson’s evenness index. FIG. 6B and FIG. 6D show a genus level assessment of unique detected microbes and Simpson’s evenness index.

[0023] FIG. 7A shows beta diversity assessment via PCoA with top three features. FIG. 7B shows a number of differentially detected microbes between asymptomatic and remission, mild, moderate, severe disease states for UC. FIG. 7C shows a critical feature assessment by PERMANOVA.

[0024] FIG. 8A and FIG. 8B show alpha diversity measurements for UC and asymptomatic patient populations. FIG. 8A shows a species level assessment of unique detected microbes. FIG. 8B shows a genus level assessment of unique detected microbes.

[0025] FIG. 9A shows a beta diversity assessment via PCoA. FIG. 9B shows a number of differentially detected microbes between asymptomatic and remission, mild, moderate, severe disease states for UC. FIG. 9C shows a critical feature assessment of PERMANOVA.

[0026] FIG. 10A, FIG. 10B, and FIG. 10C show Binary Classifier for asymptomatic / remission versus mild / moderate / severe disease for Ulcerative colitis. Classifier is assessed by receiver operating characteristics curve (ROC), as shown in FIG. 10A, and Precision recall curve, as shown in FIG. 10B. FIG. 10C shows a list is critical features as determined by SHapley Additive exPlanations (SHAP).

[0027] FIG. 11 A, FIG. 11B, and FIG. 11C show a Binary Classifier for asymptomatic / remission versus mild / moderate / severe disease for Crohn’s Disease. Classifier is assessed by ROC, as shown in FIG. 11A and Precision recall curve, as shown in FIG. 11B. FIG. 11 C shows a list is critical features as determined by SHAP.

[0028] FIG. 12A, FIG 12B, and FIG. 12C show sample distribution and disease characterization for UC patients. FIG. 12A shows the number of samples from a site with a given disease label. FIG. 12B shows the association between disease severity label (Mayo score) and modified Mayo endoscopy score (MMES). FIG. 12C shows the Mayo Endoscopy sub-score for each region of the colon for each patient (columns).

[0029] FIG. 13A, FIG. 13B, and FIG. 13C shows Ulcerative colitis patient treatment profiles. FIG. 13A shows counts for patients on a given treatment. FIG. 13B shows a correlation matrix between treatment and disease severity label. FIG. 13C shows unsupervised clustering of patients based on treatment profiles.

[0030] FIG. 14A shows the correlation of high sensitivity CRP with disease severity (Mayo score label) UC samples. The Y axis bar break occurs and continues at 200 pg / g and is used for visualization. FIG. 14B shows the correlation between fecal calprotectin with disease severity label (Mayo score label) for UC samples. The Y axis bar break occurs and continue at 10 mg / L and is used for visualization.

[0031] FIG. 15A and FIG. 15B show the distribution of abundance prior to regression of sitespecific signal. FIG. 15C and FIG. 15D show the distribution of abundance post regression of site-specific signal.

[0032] FIG. 16 shows the sum of MPM across disease severity groups for UC samples stratified by clustered treatment groups.

[0033] FIG. 17A and FIG. 17B show the enrichment of signal for stool-associated microbes from UC samples.

[0034] FIG. 18A, FIG. 18B, and FIG. 18C show a linear discriminant analysis of UC samples. Remission, mild, severe are separated upon three dimensions in a supervised manner.

[0035] FIGs. 19A-19F show a differential abundance analysis between disease severity labels for UC cohort using phylogenetically clustered microbes.

[0036] FIG. 20A and FIG. 20B show Classifier performance characteristics for the UC cohort. FIG. 20A shows an AUC-RUC plot for predicted disease severity label. AUC is determined via one versus rest methodology. FIG. 20B shows a confusion matrix of true labels versus predicted labels.

[0037] FIGs. 21A-21D show SHAP values to assess feature importance for UC based classifier.

[0038] FIG. 22A, FIG. 22B, and FIG. 22C show sample distribution and disease characterization for CD patients. FIG. 22A shows the number of samples from a site with a given disease label. FIG. 22B shows an association between disease severity label (CDAI) and simple endoscopic score for CD (SES-CD). FIG. 22C shows an SES-CD subscore for each region of the colon and ileum for each patient (Columns).

[0039] FIG. 23A, FIG. 23B, and FIG. 23C show the treatment profiles of Crohn’s disease patients. FIG. 23A shows the counts for patients on a given treatment. FIG. 23B shows a correlation matrix between treatment and CDAI. FIG. 23C shows unsupervised clustering of patients based on treatment profiles.

[0040] FIG. 24A and FIG. 24B show a correlation of fecal calprotectin and high sensitivity CRP with disease severity (CDAI). Y axis bar breaks occur and continue at 200 pg / g in FIG. 24A and at 20 mg / L in FIG. 24B, respectively. The Y axis bar breaks are used for visualization.

[0041] FIG. 25A and FIG. 25B show distribution of abundance prior to regression of site-specific signal. FIG. 25C and FIG. 25D show distribution of abundance post-regression of site-specific signal.

[0042] FIG. 26 shows the sum of MPM across disease severity groups stratified by clustered treatment groups.

[0043] FIG. 27A and FIG. 27B show the enrichment of signal for stool-associated microbes from CD samples.

[0044] FIG. 28A, FIG. 28B, and FIG. 28C show a linear discriminant analysis of CD samples. Remission, mild, moderate, severe are separated upon three dimensions in a supervised manner.

[0045] FIGs. 29A-29F shows a differential analysis between disease severity labels for a CD cohort. FIG. 29A shows a differential abundance analysis for the CD cohort with a disease severitylabel of mild remission. FIG. 29B shows a differential abundance analysis for the CD cohort with a disease severity label of moderate remission. FIG. 29C shows a differential abundance analysis for the CD cohort with a disease severity label of remission-severe. FIG. 29D shows a differential abundance analysis for the CD cohort with a disease severity label of mild-moderate. FIG. 29E shows a differential abundance analysis for the CD cohort with a disease severity label of mild- severe. FIG. 29F shows a differential abundance analysis for the CD cohort with a disease severity label of moderate-severe.

[0046] FIG. 30A and FIG. 30B show Classifier performance characteristics for the CD cohort. FIG. 30A shows an AUC-ROC plot for predicted severity label. AUC is determined via one versus rest methodology. FIG. 30B shows a confusion matrix of true labels versus predicted labels.

[0047] FIG. 31A, FIG. 31B, FIG. 31C, and FIG. 31D show SHAP values to assess feature importance for CD based classifier.

[0048] FIG. 32A and FIG. 32B show classifier performance for predicting ulcerative colitis based on down-sampled reads (10% of original). FIG. 32A is an AUC-ROC plot. FIG. 32B is a confusion matrix. FIG. 32C and FIG. 32D show classifier performance for predicting Crohn’s disease severity based on down-sampled reads (10% of original). FIG. 32C is an AUC-ROC plot. FIG. 32D is a confusion matrix.

[0049] FIGs. 33A-33I demonstrate plasma mcfDNA as an analyte to distinguish between Crohn’s disease, ulcerative colitis, and healthy / asymptomatic individuals. FIG. 33A shows a projection of samples via Bray-Curtis PCoA. FIG. 33B shows a projection of samples via linear discriminant analysis. FIG. 33C shows a differentially abundance analysis of samples from Crohn’s Disease patients and asymptomatic individuals. FIG. 33D shows a differentially abundance analysis of samples from ulcerative colitis patients and asymptomatic individuals. FIG. 33E shows a differentially abundance analysis of samples from Crohn’s disease patients and ulcerative colitis patients. Projections of samples via (A) Bray-Curtis PCoA and (B) linear discriminant analysis. (C) Differentially abundance analysis of samples from CD, UC, and asymptomatic individuals. FIG. 33F shows a classifier performance via x-cross validation. FIG. 33H shows an AUC-ROC plot to predict CD, UC, and asymptomatic labels. Classifier performance via LOSO (leave one site out) to predict CD and UC. FIG. 33G and 331 show confusion matrix performance.

[0050] FIG. 34A, FIG. 34C, and FIG. 34E show a summary of quality control metrics for ulcerative colitis cohorts. FIG. 34A shows reads passing a QC filter. FIG. 34C shows reads aligning to the human reference. FIG. 34E shows the number of deduplicated pathogen reads. FIG. 34B, FIG. 34D, and FIG. 34F shows a summary of quality control metrics for Crohn’s disease cohorts. FIG. 34B shows reads passing a QC filter. FIG. 34D shows reads aligning to thehuman reference. FIG. 34F shows the number of deduplicated pathogen reads. “AC” refers to analytical controls used in each sequencing run. “RD” refers to research samples of interest. “EC” refers to negative, non-template controls. “AC” refers to assay controls which contained a set concentration of a given set of microbes.

[0051] FIGs. 35A-35F show disease type classification performance between healthy, ulcerative colitis (UC), and Crohn’s disease (CD) (all classes of disease, remission, mild, moderate, severe). Performance was assessed via 10-fold cross-validation repeated five times across different partitions (FIGs. 35B, 35D, and 35F), and using a leave one clinical site out strategy (LOSO) (FIGs. 35A, 35C, and 35E). (FIGs. 35A-B: Microbial Classifier; FIGs. 35C-D: Human Classifier; FIGs. 35E-F: Joint Classifier).

[0052] FIGs. 36A-36C show disease type classification performance between healthy, active UC, and active CD (mild, moderate severe disease) (FIG. 36A: Microbial Classifier; FIG. 36B: Human Classifier; FIG. 36C: Joint Classifier). Performance was assessed via 10-fold cross-validation repeated five times across different partitions.

[0053] FIGs. 37A-37C show disease activity classification performance between UC disease activity groups (remission, mild moderate, severe) (FIG. 37A: Microbial Classifier; FIG. 37B: Human Classifier; FIG. 38C: Joint Classifier). Performance was assessed via 10-fold cross- validation repeated three times across different partitions.

[0054] FIGs. 38A-38C show disease activity classification between UC disease activity groups (remission, mild) versus (moderate, severe) (FIG. 38A: Microbial Classifier; FIG. 38B: Human Classifier; FIG. 38C: Joint Classifier). Performance was assessed via 10-fold cross-validation repeated three times across different partitions.

[0055] FIGs. 39A-39C show disease type classification performance between CD disease activity (remission, mild moderate, severe) (FIG. 39A: Microbial Classifier; FIG. 39B: Human Classifier; FIG. 39C: Joint Classifier). Performance was assessed via 10-fold cross-validation repeated three times across different partitions.

[0056] FIGs. 40A-40C show disease type classification performance between CD disease activity groups (remission, mild) versus (moderate, severe) (FIG. 40A: Microbial Classifier; FIG. 40B: Human Classifier; FIG. 40C: Joint Classifier). Performance was assessed via 10-fold cross- validation repeated three times across different partitions.

[0057] FIG. 41 shows a computer control system that is programmed or otherwise configured to implement methods provided herein.DETAILED DESCRIPTION OF THE INVENTION

[0058] The following passages describe different aspects of the disclosure in greater detail. Each aspect, embodiment, or feature of the disclosure can be combined with any other aspect, embodiment, or feature of the disclosure unless clearly indicated to the contrary.Definitions

[0059] Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this disclosure belongs.

[0060] The articles “A,” “an,” and “the”, as used herein, can each include singular or plural references unless expressly limited to one reference, or unless otherwise indicated by context.

[0061] As used herein, the term “or” is used to refer to a nonexclusive “or”; as such, “A or B” includes “A but not B,” “B but not A,” and “A and B,” unless otherwise indicated.

[0062] As used in the specification herein, unless otherwise indicated, the term "about" generally means plus or minus ten percent (10%) of a value, inclusive of the value, unless otherwise indicated by the context of the usage. For example, “about 100” refers to any number from 90 to 110 and includes the number 100, unless otherwise indicated by the context in which the term is used. The term “about” a range refers to that range minus 10% of its lowest value and plus 10% of its greatest value. When the term "about" is used before a non-numerical term that is a stand- in for a numerical value (e.g., horizontal, perpendicular, aligned), the term "about" refers to the value of the non-numerical term (e.g., 90 degrees, 1800 degrees) plus or minus 10% of that value.

[0063] Whenever the term "at least," "greater than," "greater than or equal to," "no more than," "less than," or "less than or equal to” (or any of their equivalents) precedes the first numerical value in a series of two or more numerical values, the term applies to each of the numerical values in that series of numerical values, unless otherwise specified. For example, greater than or equal to 1, 2, or 3 is equivalent to greater than or equal to 1, greater than or equal to 2, or greater than or equal to 3.

[0064] Whenever the term "no more than," "less than," or "less than or equal to" (or any of their equivalents) precedes the first numerical value in a series of two or more numerical values, the term "no more than," "less than," or "less than or equal to" applies to each of the numerical values in that series of numerical values. For example, less than or equal to 3, 2, or 1 is equivalent to less than or equal to 3, less than or equal to 2, or less than or equal to 1.

[0065] The terms “increased,” “increasing,” or “increase” are used herein to generally mean an increase by a statically significant amount. In some cases, the terms “increased” or “increase” mean an increase of at least 10% as compared to a reference level, for example an increase of at least about 10%, at least about 20%, or at least about 30%, or at least about 40%, or at least about50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% increase or any increase between 10-100% as compared to a reference level, standard, or control. Other examples of “increase” include an increase of at least 2-fold, at least 5-fold, at least 10-fold, at least 20-fold, at least 50-fold, at least 100-fold, at least 1000-fold or more as compared to a reference level.

[0066] The terms, “decreased,” “decreasing,” or “decrease” are used herein generally to mean a decrease by a statistically significant amount. In some cases, “decreased” or “decrease” means a reduction by at least 10% as compared to a reference level, for example a decrease by at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% decrease (e.g., absent level or non-detectable level as compared to a reference level), or any decrease between 10-100% as compared to a reference level. In the context of a marker or symptom, by these terms is meant a statistically significant decrease in such level. The decrease can be, for example, at least 10%, at least 20%, at least 30%, at least 40% or more, and is preferably down to a level accepted as within the range of normal for an individual without a given disease.

[0067] Throughout this application, various cases may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the disclosure. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.

[0068] As used herein, “abundance” refers to the quantity of something, such as, for example, the quantity or number of molecules, such as nucleic acids. As used herein, “relative abundance” is the abundance of a molecule or molecules of interest per abundance of a reference molecule or molecules of interest. For example, relative abundance of target nucleic acid molecules (e.g., microbial cell-free nucleic acids) refers to abundance per reference nucleic acids (e.g., host nucleic acids, synthetic nucleic acid added to the sample, etc.). As used herein, “absolute abundance” is the abundance of molecules per a defined unit of initial sample or sample quantity. For example, absolute abundance of target nucleic acid molecules (e.g., microbial cell-free nucleic acids) refers to the abundance per defined unit of sample quantity (e.g., sample volume, sample mass etc.).

[0069] As used herein, “adapter” or “portions of an adapter” refers to a chemically synthesized, single-stranded, or double-stranded oligonucleotide that can be attached, e.g., covalently (e.g., ligation, primer extension) or non-covalently (e.g., hybridization), to the ends of nucleic acid molecules, such as DNA or RNA molecules. Adapter sequences can be of any length. Adapter can refer to either a full-length adapter or a portion of the adapter, e.g., partial adapters can be attached in some embodiments before the full-lengths are introduced by e.g., indexing primers in amplification steps. 3'-end adapters and 5'-end adapters can be full-length or a portion of an adapter sequence that are attached to the opposite ends of a target nucleic acid, a copy of a target nucleic acid, or a target nucleic acid complement. 3'-end adapters and 5'-end adapters sequences end up being attached to the opposite ends of e.g., a template that can be sequenced that comprises target nucleic acid, a copy of a target nucleic acid, and / or a target nucleic acid complement. The 3'-end adapter and 5'-end adapter sequences can be the same or they can be different.

[0070] As used herein, “antibody” refers to a type of immunoglobulin molecule and is used in the broadest sense to include intact antibodies as well as antibody fragments. As used herein, antibodies comprise at least one antigen-binding domain. For example, an antibody as described herein can have an antigen binding domain or antigen binding region, the antigen binding domain or antigen binding region being specific for an antigen. In some embodiments, the antigen is a bulky moiety, such as digoxigenin.

[0071] As used herein, “bulky moiety” refers to a molecule that takes up more space than is conventionally required or a molecule that forms a complex that takes up more space than is conventionally required. A bulky moiety may comprise any reactive group capable of forming covalent, non-covalent, or coordinating chemical bonds. In some embodiments, the bulky moiety comprises one or more azide groups and products of reactions with azide groups, one or more small molecules, one or more polyhistidine tags, one or more antigens, and / or one or more proteins. In some embodiments, the bulky moiety comprises digoxigenin. A bulky moiety for example, can include a functional group that is sterically hindering and can prevent certain enzymatic or chemical reactions from occurring. A bulky group can block a position. A bulky group can also affect a molecule's shape and reactivity and so prevent a reaction from occurring through the steric hindrance. Moieties attached to the groups by covalent, non-covalent or coordinating bonds can provide the bulkiness of the groups. For example, a bulky molecule such as a protein or polymer can be attached covalently to an azide group; a bulky entity such as a bead, protein or polymer can be attached to a his tag through coordinating bonds using Ni ions; or an antigen antibody can be attached to an antigen attached to an adapter such as an anti-digoxigenin antibody can be attached to digoxigenin. Examples of bulky moieties can also include, but are not limited to, complexesbetween any of the molecules disclosed herein and their respective binding and reaction partners including, for example, without limitation, complexes between digoxigenin and an anti- digoxigenin antibody; polyhistidine tag and aNi-NTA-containing polymer; a protein and a binding partner; an azide group and a covalently bound large molecule; and the biotin and streptavidin complex. Additional examples of bulky molecules include, for example, without limitation, biotin, azide groups and products of reactions with azide groups, one or more small molecules, one or more polyhistidine tags, and / or one or more proteins. Some embodiments further comprise introducing a bulky moiety into the splint oligonucleotide. Some embodiments further comprise introducing a bulky moiety on the template switching oligos; such bulky moieties can reduce concatemer formation. The bulky moiety can be introduced at a position that has the lowest effect on adapter attachment efficiency, such as the 5'-end region of the splint oligonucleotide, close to the 5'-end region of the splint oligonucleotide, or away from the ligation junction in ligation-based adapter attachment reactions.

[0072] As used herein, “control” refers to a standard of comparison. A “negative control” refers to a standard of comparison that is used to identify contaminants from samples, or to identify the nature of a signal in the absence of a sample (e.g., a background signal). A “positive control” refers to a standard of comparison that is designed to produce a positive result or signal. Generally, the presence of a substance (e.g., nucleic acid) is detected in a positive control that is run during an assay. Some embodiments of the disclosure comprise a positive and / or negative control. Some embodiments of the disclosure comprise an initial sample or samples without a positive and / or negative control. Some embodiments of the disclosure comprise an initial sample or samples without a positive control. Some embodiments of the disclosure comprise an initial sample or samples without a negative control.

[0073] As used herein, “denaturing” refers to a process in which biomolecules, such as proteins or nucleic acids, lose their native or higher order structure. Native and higher order structure can include, for example, without limitation, quaternary structure, tertiary structure, or secondary structure. For example, a double-stranded nucleic acid molecule can be denatured into two singlestranded molecules.

[0074] As used herein, the term “dephosphorylation” or “dephosphorylating” refers to removal of a terminal phosphate group, such as the 5'- and / or 3'-end phosphate, from a nucleic acid, such as DNA to generate 5'- and / or 3'-hydroxyl groups.

[0075] As used herein, “detect” refers to quantitative or qualitative detection, including, without limitation, detection by identifying the presence, absence, quantity, frequency, concentration, sequence, form, structure, origin, or amount of an analyte.

[0076] As used herein, “digoxigenin” refers to a bulky molecule or its complex comprising thestructure:

[0077] As used herein, “GC-bias” refers to differential performance (e.g., amplification) or treatment of nucleic acids having different GC content but identical length.

[0078] As used herein, “GC-content” or “guanine-cytosine content” refer to the percentage or quantity of nitrogenous bases in a nucleic acid, such as a DNA or RNA molecule, that are either guanine or cytosine or their chemical modifications.

[0079] As used herein, “host” refers to an organism that harbors another organism or microbe. For example, a living thing e.g. a mammal such as a human being can be a host that harbors a microbe or pathogen, the microbe or pathogen being the non-host.

[0080] As used herein, the phrase “identifying sequence element” or “identifying tag” refers to an element of a sequence that identifies an index, a code, a barcode, a random sequence, an adapter, an overhang of non-templated nucleic acids, a tag comprising one or more non-templated nucleotides, a priming sequence, unique molecular identifiers, or any combination thereof.

[0081] As used herein, “isolation” or “purification” and their cognates, of nucleic acids refers to steps (e.g., elution) after the start of and in the generation of a nucleic acid library that separate the nucleic acid from at least one component with which it is normally associated (e.g., a ligase or a polymerase).

[0082] As used herein, “KI enow fragment” refers to a large protein fragment of DNA polymerase I that retains the 5' 3' polymerase activity and the 3' 5' exonuclease activity for removal of precoding nucleotides and proofreading but loses its 5' 3' exonuclease activity.

[0083] As used herein, “ligating” or “ligation” refers to the joining of two ends of nucleic acid fragments through the action of an enzyme. DNA molecules and RNA molecules can be ligated. There are many methods of ligation and one skilled in the art would readily understand methods of ligation other than those disclosed herein.

[0084] As used herein, “length bias” refers to a bias with respect to length of a particular nucleic acid size or fragment length created by a sequencing library generation process as opposed to another size or fragment length. It can be preferable to reduce length bias for consistent or moreaccurate results. In some aspects, it can be preferable to increase a length bias for a certain range or against a certain range.

[0085] As used herein, “pathogen” refers to a microbe that can cause a disease, ailment, or an infection.

[0086] As used herein, “microbe,” or “microbial,” generally refers to archaea, bacteria, fungi, protists, parasites, viruses, or other entities that are usually detectable using a microscope (e.g., an optical microscope or electron microscopy). As used herein, the term “microorganism” refers to a uni- or multi- cellular organism, such as, for example, a microscopic organism or macroscopic organism including but not limited to bacteria, fungi, protists, and parasites. Microbes herein can be a prokaryote or a eukaryote. Microbes are often pathogens responsible for disease, but can also exist in a non-pathogenic, symbiotic, commensalistic, mutualistic, or amensalistic relationship with a host, such as a human.

[0087] Examples of microbes include one or more species or strains from one or more of the following genera: Coniosporium, Hantavirus, Talaromyces, Machlomovirus, Betatetravirus, Raoultella, Aeromonas, Ephemerovirus, Empedobacter, Loa, Macluravirus, Stenotrophomonas, Alfamovirus, Rosavirus, Emmonsia, Aggregatibacter, Orthopneumovirus, Weeksella, Nairovirus, Salivirus, Weissella, Mosavirus, Gammapartitivirus, Strongyloides, Passerivirus, Erysipelatoclostridium, Bacillarnavirus, lotatorquevirus, Taenia, Trypanosoma, Olsenella, Cladosporium, Rhizobium, Prevotella, Leclercia, Paracoccus, liarvirus, Lagovirus, Rasamsonia, Plasmodium, Acremonium, Chlamydia, Clonorchis, Vibrio, Bartonella, Nakazawaea, Franconib acter, Anisakis, Norovirus, Nocardia, Solobacterium, Parechovirus, Avenavirus, Orthohepevirus, Aphthovirus, Hepandensovirus, Microbacterium, Lichtheimia, Lomentospora, Achromob acter, Ipomovirus, Tsukamurella, Elizabethkingia, Hepevirus, Seadornavirus, Altemaria, Trueperella, Gammatorquevirus, Bifidobacterium, Chrysosporium, Thogotovirus, Curtovirus, Deltatorquevirus, Balamuthia, Mastrevirus, Bdellomicrovirus, Mupapillomavirus, Pseudozyma, Wickerhamiella, Aquamavirus, Alloscardovia, Thielavia, Idaeovirus, Henipavirus, Coxiella, Haemophilus, Gammacoronavirus, Negevirus Brevibacterium, Peptoniphilus, Alphacarmotetravirus, Nosema, Trichovirus, Arenavirus, Thermomyces, Necator, Waikavirus, Blosnavirus, Jonesia, Tetraparvovirus, Emaravirus, Plectrovirus, Sclerodamavirus, Toxocara, Umbravirus, Burkholderia, Chromobacterium, Paracoccidioides, Brugia, Eragrovirus, Macrococcus, Absidia, Colletotrichum, Inovirus, Phycomyces, Wickerhamomyces, Acidaminococcus, Moraxella, Rothia, Phlebovirus, Slackia, Purpureocillium, Betapapillomavirus, Tupavirus, Cryspovirus, Saksenaea, Erysipelothrix, Kobuvirus, Mimoreovirus, Echinococcus, Mannheimia, Bergeyella, Cyclospora, Xylanimonas, Leptospira, Finegoldia, Curvularia,Cryptosporidium, Babuvirus, Pecluvirus, Lambdatorquevirus, Pythium, Carlavirus, Entomobimavirus, Kocuria, Anaplasma, Ampelovirus, Avihepatovirus, Nepovirus, Rhodococcus, Bordetella, Mischivirus, Scedosporium, Gardnerella, Maculavirus, Trichoderma, Aveparvovirus, Salmonella, Avastrovirus, Copiparvovirus, Trachipleistophora, Clostridioides, Nanovirus, Siccibacter, Leptotrichia, Citrivirus, Odoribacter, Sanguibacter, Novirhabdovirus, Acremonium, Hafnia, Chaetomium, Tenuivirus, Yokenella, Rubulavirus, Varicellovirus, Alphamesonivirus, Sicinivirus, Leuconostoc, Microvirus, Gallantivirus, Morbillivirus, Lolavirus, Pantoea, Hepatovirus, Nupapillomavirus, Metschnikowia, Bamavirus, Kytococcus, Tritimovirus, Tannerella, Respirovirus, Pneumocystis, Dirofilaria, Pediococcus, Lactococcus, Blastomyces, Dianthovirus, Actinobacillus, Teschovirus, Oscivirus, Begomovirus, Potyvirus, Byssochlamys, Alphacoronavirus, Molluscipoxvirus, Lymphocryptovirus, Sapelovirus, Parabacteroides, Pyrenochaeta, Listeria, Senecavirus, Brevidensovirus, Potexvirus, Parvimonas, Flavivirus, Recovirus, Toxoplasma, Yatapoxvirus, Opisthorchis, Trichuris, Cyphellophora, Morganella, Perhabdovirus, Micrococcus, Pequenovirus, Mastadenovirus, Anaeroglobus, Tropheryma, Dolosigranulum, Wolbachia, Lelliottia, Mycoplasma Tobravirus, Shewanella, Paeniclostridium, Erythroparvovirus, Sutterella, Sporopachydermia, Namavirus, Nyavirus, Francisella, Arthroderma, Epsilontorquevirus, Sigmavirus, Amdoparvovirus, Actinomyces, Alphapermutotetravirus, Cardiobacterium, Influenzavirus C, Orthopoxvirus, Poacevirus, Phialophora, Lactobacillus, Polyomavirus, Debaryomyces, Foveavirus, Bymovirus, Mycoflexivirus, Grimontia, Mucor, Rhytidhysteron, Quadrivirus, Thermoascus, Aureusvirus, Trichosporon, Myceliophthora, Dermacoccus, Dysgonomonas, Pseudoramibacter, Becurtovirus, Gordonia, Sapovirus, Orthobunyavirus, Spiromicrovirus, Pomovirus, Exophiala, Sneathia, Helicobacter, Photorhabdus, Mogibacterium, Betapartitivirus, Avibimavirus, Ambidensovirus, Oleavirus, Orientia, Deltacoronavirus, Anulavirus, Trichomonasvirus, Budvicia, Geotrichum, Enamovirus, Lachnoclostridium, Schistosoma, Paecilomyces, Panicovirus, Rhizoctonia, Brevibacillus, Beauveria, Pestivirus, Tombusvirus, Cilevirus, Cokeromyces, Peptostreptococcus, Phanerochaete, Proteus, Idnoreovirus, Aspergillus, Pasteurella, Malassezia, Hanseniaspora, Endornavirus, Azospirillum, Velarivirus, Cystovirus, Avisivirus, Bacteroides, Picobirnavirus, Myroides, Circovirus, Arterivirus, Aquaparamyxovirus, Onchocerca, Cosavirus, Kluyveromyces, Fijivirus, Candida, Hepacivirus, Dermabacter, Ourmiavirus, Allexivirus, Enterobacter, Acidovorax, Bracorhabdovirus, Carmovirus, Pluralibacter, Coltivirus, Fonsecaea, Streptobacillus, Corynebacterium, Macrophomina, Marburgvirus, Comovirus, Fabavirus, Alphanodavirus, Cellulomonas, Enterobius, Catabacter, Moellerella, Nakaseomyces, Cucumovirus, Valsa, Deltapartitivirus, Plesiomonas, Pseudomonas, Torovirus, Cuevavirus, Hypovirus, Trichomonas,Influenzavirus D, Giardiavirus, Crinivirus, Tepovirus, Sakobuvirus, Cyberlindnera, Paenalcaligenes, Bafinivirus, Rymovirus, Pegivirus, Yarrowia, Treponema, Borreliella, Rubivirus, Aureobasidium, Angiostrongylus, Filobasidium, Photobacterium, Rhizopus, Orthoreovirus, Ustilago, Simplexvirus, Aquareovirus, Protoparvovirus, Propionibacterium, Sprivivirus, Hunnivirus, Apophysomyces, Meyerozyma, Alphapapillomavirus, Candida, Brucella, Gallivirus, Dinovemavirus, Anaerobiospirillum, Eubacterium, Tatlockia, Terrisporobacter, Quaranjavirus, Sobemovirus, Dicipivirus, Arcanobacterium, Macanavirus, Atopobium, Vesivirus, Lodderomyces, Dinornavirus, Betatorquevirus, Kerstersia, Aparavirus, Neisseria, Agrobacterium, Edwardsiella, Labymavirus, Totivirus, Actinomadura, Tobamovirus, Influenzavirus B, Mandarivirus, Anaerococcus, Kunsagivirus, Naegleria, Campylobacter, Veillonella, Yamadazyma, Filobasidiella, Oerskovia, Penicillium, Anncaliia, Leptosphaeria, Pneumovirus, Psychrobacter, Isavirus, Granulicatella, Torradovirus, Cladophialophora, Influenzavirus A, Ophiostoma, Aerococcus, Ureaplasma, Etatorquevirus, Bocaparvovirus, Megasphaera, Reptarenavirus, Comamonas, Capnocytophaga, Alphatorquevirus, Syncephalastrum, Wallemia, Betacoronavirus, Hyphopichia, Nocardiopsis, Legionella, Trichinella, Paraburkholderia, Mammarenavirus, Echinostoma, Sphingobacterium, Enterovirus, Methanobrevibacter, Ochroconis, Cheravirus, Pasivirus, Enterococcus, Mycoreovirus, Tospovirus, Betanodavirus, Phytoreovirus, Enterocytozoon, Ferlavirus, StemphyliumFilifactor, Leishmaniavirus, Gemella, Bromovirus, Alloiococcus, Cunninghamella, Cronobacter, Oribacterium, Orbivirus, Chrysovirus, Cripavirus, Tatumella, Pandoraea, Ogataea, Dracunculus, Volvariella, flavirus, Benyvirus, Rhadinovirus, Histoplasma, Rahnella, Morococcus, Verticillium, Janibacter, Gyrovirus, Alphapartitivirus, Mycobacterium, Roseomonas, Varicosavirus, Chryseobacterium, Parapoxvirus, Rhizomucor, Aureimonas, Levivirus, Leishmania, Luteovirus, Cypovirus, Ochrobactrum, Microsporum, Piscihepevirus, Ceratocystis, Sporothrix, Vesiculovirus, Cupriavidus, Cryptococcus, Metapneumovirus, Alphanecrovirus, Eikenella, Brevundimonas, Escherichia, Leifsonia, Schizophyllum, Granulibacter, Gordonibacter, Lachancea, Madurella, Ophiovirus, Phellinus, Nebovirus, Acanthamoeba, Fusobacterium, Pichia, Verruconis, Ehrlichia, Tibrovirus, Higrevirus, Wohlfahrtiimonas, Rhinocladiella, Neorickettsia, Sadwavirus, Roseobacter, Sequivirus, Pannonibacter, Rotavirus, Turicella, Cardiovirus, Propionimicrobium, Furovirus, Naumovozyma, Closterovirus, Fluoribacter, Zeavirus, Clavispora, Megrivirus, Gammapapillomavirus, Rickettsia, Polemovirus, Corynespora, Encephalitozoon, Shimwellia, Fusarium, Yersinia, Capronia, Delftia, Victorivirus, Marafivirus, Kluyvera, Iteradensovirus, Isoptericola, Vitivirus, Roseolovirus, Conidiobolus, Abiotrophia, Babesia, Phoma, Sanguibacteroides, Staphylococcus, Rhodotorula, Zetatorquevirus, Hymenolepis, Fasciola,Cytorhabdovirus, Cardoreovirus, Memnoniella, Trichophyton, Mitovirus, Phaeoacremonium, Providencia, Lysinibacillus, Giardia, Oligella, Streptomyces, Paracl ostridium, Ralstonia, Coccidioides, Brambyvirus, Biatriospora, Allolevivirus, Acinetobacter, Starmerella, Omegatetravirus, Porphyromonas, Avulavirus, Streptococcus, Arcobacter, Topocuvirus, Mamastrovirus, Ancylostoma, Bomavirus, Capillovirus, Alphavirus, Tymovirus, Nucleorhabdovirus, Diaporthe, Chlamydiamicrovirus, Tumcurtovirus, Saccharomyces, Riemerella, Betanecrovirus, Clostridium, Mobiluncus, Cercospora, Mamavirus, Mortierella, Aquabimavirus, Xanthomonas, Dependoparvovirus, Ebolavirus, Neofusicoccum, Borrelia, Leminorella, Klebsiella, Blastocystis, Alcaligenes, Citrobacter, Eggerthella, Cedecea, Serratia, Penstyldensovirus, Bacillus, Laribacter, Wuchereria, Hordeivirus, Cytomegalovirus, Actinomucor, Ascaris, Shigella, Vittaforma, Torulaspora, Kingella, Oryzavirus, Polerovirus, Tremovirus, Erbovirus, Entamoeba, Lyssavirus, Paenibacillus, Facklamia, Kappatorquevirus, Metarhizium, Stachybotrys, Okavirus, Botrexvirus, Thetatorquevirus, and Basidiobolus.

[0088] Microbes or pathogens can include archaea, bacteria, yeast, fungi, molds, protozoans, nematodes, eukaryotes, and / or viruses. Microbes or pathogens can also include DNA viruses, RNA viruses, culturable bacteria, additional fastidious and unculturable bacteria, mycobacteria, and eukaryotic pathogens (See, Bennett et al., Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, Ninth Edition; Elsevier, 2019; and Netter's Infectious Disease, 2nd Edition, Jong and Stevens, eds. Elsevier, 2021). Microbes or pathogens can also include any of the microbes known to a person of skill.

[0089] As used herein, “microbe,” or “microbial,” generally refers to bacteria, fungi, protists, parasites, viruses, or other entities that are usually detectable using a microscope. As used herein, the term “microorganism” refers to a uni- or multi- cellular organism, such as, for example, a microscopic organism or macroscopic organism including but not limited to bacteria, fungi, protists, and parasites. Microbes are often pathogens responsible for disease, but can also exist in a non-pathogenic, symbiotic, commensalistic, mutualistic, or amensalistic relationship with a host, such as a human.

[0090] As used herein, “nucleic acid” refers to a polymer or oligomer of nucleotides and is generally synonymous with the term “polynucleotide” or “oligonucleotide.” Nucleic acids may comprise a deoxyribonucleotide, a ribonucleotide, a deoxyribonucleotide analog, chemically modified canonical deoxyribonucleotides, ribonucleotides, and / or ribonucleotide analog, nucleic acids with modified backbones, or any combination thereof.

[0091] Nucleic acids can be of any length. The following are non-limiting examples of nucleic acids: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkageanalysis, exons, introns, messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), short interfering RNA (siRNA), short-hairpin RNA (shRNA), micro-RNA (miRNA), long non coding RNA (Inc RNA), small non coding RNAs such as but not restricted to piwi RNAs and enhancer RNAs, circ RNA (circular RNA), ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, primers, mitochondrial DNA, circulating nucleic acids, cell-free nucleic acids, cfDNA, cfNA, host cfNA, non-host cfNA, circulating cfNA, microbial cell free nucleic acids, viral nucleic acid, bacterial nucleic acid, genomic DNA, pathogen nucleic acids, fungal nucleic acid, parasitic nucleic acid, exosomal nucleic acid, intercellular signal nucleic acid, exogenous nucleic acids, nucleic acid therapeutics, and DNA enzymes. A nucleic acid may comprise one or more modified nucleotides, such as methylated nucleotides or methylated nucleotide analogs. If present, modifications to the structure can be imparted before or after assembly of the polymer. The sequence of nucleotides can be interrupted by non-nucleotide components. A nucleic acid can be further modified after polymerization, such as by conjugation with a labeling component. A nucleic acid can be single-stranded, double-stranded, have higher numbers of strands (e.g, triple- stranded), and / or have a higher order of structure (e.g, tertiary, or quaternary structure). A target nucleic acid can be any type, category, or subcategory of nucleic acids.

[0092] As used herein, “removal” or “extraction,” and their cognates, of nucleic acids refers to steps prior to the start of generating or preparing a nucleic acid library that separate nucleic acids from at least one component with which they are normally associated. Removal or extraction of nucleic acids can refer to the process of creating an initial sample from a raw biological sample. For example, without limitation, the fractionation of whole blood into its component parts, such as plasma, can be considered to involve removal or extraction. Similarly, purification or isolation of DNA from a sample (e.g., plasma sample) can be considered extraction.

[0093] The term “sequencing,” as used herein, generally refers to methods and technologies for determining the sequence of nucleotide bases in one or more polynucleotides. Sequencing can involve basic methods including Maxam-Gilbert sequencing and chain-termination methods, or de novo sequencing methods including shotgun sequencing and bridge PCR, or next-generation sequencing (NGS) methods (or massively-parallel sequencing method) including but not limited to polony sequencing, pyrosequencing, sequencing-by-synthesis, sequencing by ligation, ion semiconductor sequencing, single molecule sequencing, single-molecule real-time sequencing, nanopore sequencing, and others. Sequencing can be performed by various systems currently available, such as, without limitation, a sequencing system by Illumina®, Pacific Biosciences®,Oxford Nanopore®, Genia Technologies®, or Life Technologies® and others. Such devices can provide a plurality of raw genetic data corresponding to the genetic information of a host (e.g., human), a non-host (e.g., a pathogen, an organ donor), a host-derived variant genetic sequence (e.g., a single nucleotide polymorphism), and / or combinations thereof as generated by the device from a sample provided by the subject.

[0094] The term “derived from” encompasses the terms “originated from,” “obtained from,” “obtainable from” and “created from,” and generally indicates that one specified material finds its origin in another specified material or has features that can be described with reference to the specified material. For example, a sample can be derived from a blood draw, a nucleic acid can be derived from a sample, a sequence read can be derived from sequencing a nucleic acid, or any combination thereof.

[0095] As used herein, the phrase “uniformly distributed” refers to a distribution that is continuous or uniform between members of a family such that for each member of a family there is a predictable or symmetric interval between them. The term “non-uniformly distributed” refers to a distribution of members of a family that does not have a predictable or symmetric interval between them.Overview

[0096] This disclosure provides, in some embodiments, methods of using a sample comprising cell-free nucleic acids (cfNA) to assess the type and / or severity of gastrointestinal disorders such as inflammatory bowel disease. In some embodiments, the subject may be a human subject. In some cases, the methods can be practiced using samples that are not feces, such as plasma. In some instances, the methods can distinguish between two or more different types of conditions, such as two different subtypes of inflammatory bowel disease. For example, in some embodiments, the methods provided herein can distinguish between ulcerative colitis (UC) and Crohn’s disease (CD), or can distinguish between UC, CD, and healthy. Distinguishing between different types of disease can, in some embodiments, inform a treatment regimen so that the treatment can be better tailored for the type of disease identified. In some instances, the methods provided herein can also differentiate diseases based on relative severity. In some embodiments, the methods can distinguish between severe, moderate, mild, in remission, or healthy conditions. In some embodiments, differentiation based on severity can inform a treatment regimen. In some embodiments, the method comprises enriching a sample for cfNA of a particular size, degradation status, and strandedness. For example, in some cases, the method comprises enriching cfNA for lengths between about 10 bases and 200 bases. In some embodiments, the method comprises producing a single-stranded library by denaturing double-stranded and single-stranded fragmentsin a sample of cfNA so that the sample comprises single-stranded fragments present in the original sample as well as single-stranded fragments resulting from denaturing the double-stranded fragments. In some embodiments, the method does not comprise enriching a sample.

[0097] This disclosure also provides microbial and / or mammalian (e.g., human) classifiers for differentiating between types or severity of disease. In some instances, the classifiers are based on microbial cell-free nucleic acid (e.g., mcfDNA) and / or mammalian (e.g., human) cfNA (e.g., human cfDNA, circulating mRNA) signatures that are able to distinguish between different types of conditions (e.g., between ulcerative colitis, Crohn’s disease and / or healthy conditions). In some instances, the classifiers are based on microbial cell-free nucleic acid (e.g., mcfDNA) and / or mammalian (e.g., human) NA (e.g., human cfDNA, circulating mRNA) signatures that are able to distinguish between different severities of a condition (e.g., between healthy, remission, mild disease, moderate disease, or severe disease). In some embodiments, the microbial cell-free nucleic acid (e.g., mcfDNA) signatures reflect microbes at the level of species, strain, genus, family, order, class, order, phylum, and / or kingdom. In some cases, the mammalian or human signatures contain one or more biomarkers that are gene-level biomarkers, pathway-level biomarkers, or a combination thereof. In some embodiments, a plurality of biomarkers are controlled by a common regulatory element.

[0098] The classifiers provided herein may also, in some cases, be based on mammalian or human fragmentomics signatures. In some embodiments, the mammalian or human fragmentomic signature reflects non-random patterns present in cell-free nucleic acids (e.g., cfDNA). Some examples of fragmentomic features include, but are not limited to, location, size, orientation, motifs, and / or cut-site motifs. In some embodiments, the classifiers can be based on analysis of cell-free nucleic acids (e.g., human cfDNA) associated with genes, promoters, and / or enhancers, as an indication of gene activation. In some cases, the fragmentomics markers are gene-level biomarkers, pathway-level biomarkers, or a combination thereof.

[0099] In some instances, the classifiers are based on microbial cell-free nucleic acid (e.g., mcfDNA) signatures and subject cell-free nucleic acid (e.g., subject cfDNA) signatures that, in combination, are able to distinguish between different types of conditions (e.g., between ulcerative colitis, Crohn’s disease and healthy conditions). In some instances, the classifiers are based on microbial cell-free nucleic acid (e.g., mcfDNA) signatures and subject cell-free nucleic acid (e.g., subject cfDNA) signatures that, in combination, are able to distinguish between different severities of a condition (e.g., between healthy, remission, mild disease, moderate disease, and / or severe disease, or a combination thereof). In some embodiments, the methods comprise combining data obtained from processing of subject cell-free DNA and data obtained from processing of microbialcell-free DNA. In some embodiments, a subject may be a human subject. In addition, the methods disclosed herein may comprise combining data obtained from processing of subject cell-free DNA or microbial cell-free DNA and data obtained from any one or more other diagnostic methods or medical means, such as medical records, symptoms, or vital signs, etc.

[0100] In some cases, the cell-free nucleic acids (e.g., cfDNA) are sequenced (e.g., by massively parallel sequencing, NGS, or beyond NGS) to obtain sequence reads. The sequence reads can be used to identify microbial sequences and / or human sequences in a sample. The microbial sequences can be used to detect microbes at a species, strain, genus, family, order, class, order, phylum, and / or kingdom level. The human sequences can be used to identify human genes that are dysregulated (e.g., upregulated or downregulated) in a particular condition. In some instances, the identification of dysregulated genes is based on a fragmentomics analysis, particularly fragmentomics of cfDNA at regulatory elements such as promoters. In some embodiments, the human and microbial cell-free nucleic acids are present as a combination within a single sample and are maintained in the single sample through sequencing analysis. In some embodiments, a single sample containing a combination of human and microbial cell-free nucleic acids is divided and separately processed, with one of the samples analyzed for microbial cell-free nucleic acids, while another sample is analyzed for subject cell-free nucleic acids. In some cases, samples can be processed differently; for example, one sample can be physically enriched for a certain length of DNA or RNA, and one sample can be physically enriched for a different length of DNA or RNA.

[0101] In some embodiments, one or more features of data may be identified via processing of subject cell-free DNA and / or microbial cell-free DNA, and such data can, in some instances, be aggregated or combined. In some embodiments, a classifier is trained on input of data obtained from processing of subject cell-free DNA or microbial cell-free DNA. In some embodiments, a classifier may be trained on input of data obtained from processing of both subject cell-free DNA and microbial cell-free DNA. In some cases, the subject may be a human subject. In some cases, the classifier is trained on data indicating a type of microbe and / or the identity of one or more dysregulated genes.

[0102] This disclosure provides, in some embodiments, methods of using a sample physically enriched for microbial cell-free nucleic acids (e.g., microbial cell-free DNA) or relatively short fragments of mammalian cell-free nucleic acids (e.g., relatively short fragments of subject cell- free DNA) to assess the type and / or severity of gastrointestinal disorders such as inflammatory bowel disease. In some embodiments, the methods comprise physically enriching cfNA by size selection using a size-selection method described herein. In some embodiments, size selectioncomprises applying the cfNA to a solid support (e.g., magnetic beads). In some embodiments, the methods can comprise enriching for degraded nucleic acid fragments. In some embodiments, the degraded nucleic acid fragments comprise degraded double-stranded cfNA (degraded dscfNA) or degraded single-stranded cfNA (degraded sscfNA). In some embodiments, the subject may be a human subject. In some cases, the methods can be practiced using samples that are not feces, such as plasma. In some instances, the methods can distinguish between two or more different types of conditions, such as two different types of inflammatory bowel disease. For example, in some embodiments, the methods provided herein can distinguish between ulcerative colitis and Crohn’s disease, or can distinguish between ulcerative colitis, Crohn’s disease, and healthy. Distinguishing between different types of disease can, in some embodiments, inform a treatment regimen so that the treatment can be better tailored for the type of disease identified. In some instances, the methods provided herein can also differentiate disease based on relative severity. For example, the methods provided herein can, in some cases, can distinguish between severe, moderate, mild, in remission, or healthy conditions. Differentiation based on severity can, in some embodiments, inform a treatment regimen. In some embodiments, the method does not comprise enriching a sample.

[0103] This disclosure provides, in some embodiments, methods of using a sample comprising a plurality of cell-free nucleic acids (cfNA) of different sources or strandedness to assess the type and / or severity of gastrointestinal disorders, such as inflammatory bowel disease. In some embodiments, the plurality of the cfNA can comprise subject cell-free nucleic acids (subject cfNA), microbial cell-free nucleic acids (mcfNA), or a mixture thereof. In some embodiments, the cfNA comprises double-stranded cfNA, single-stranded cfNA, degraded double-stranded cfNA (degraded dscfNA) and / or degraded single-stranded cfNA (degraded sscfNA). In some embodiments, the methods comprise denaturing the double-stranded cfNA and / or the degraded dscfNA into single-stranded fragments. In some embodiments, the methods comprise preparing a single-stranded DNA library from the denatured cfDNA. In some embodiments, the methods comprise physically enriching short or degraded nucleic acids. In some embodiments, the methods can distinguish between two or more different types of conditions, such as two different types of inflammatory bowel disease. For example, in some embodiments, the methods provided herein can distinguish between ulcerative colitis and Crohn’s disease, or can distinguish between ulcerative colitis, Crohn’s disease, and healthy. Distinguishing between different types of disease can, in some embodiments, inform a treatment regimen so that the treatment can be better tailored for the type of disease identified. In some instances, the methods provided herein can also differentiate disease based on relative severity. For example, the methods provided herein can, insome cases, can distinguish between severe, moderate, mild, in remission, or healthy conditions. Differentiation based on severity can, in some embodiments, inform a treatment regimen. In some embodiments, the method does not comprise enriching a sample.

[0104] The methods provided herein can be applied in various ways to aid the care of patients with IBD. In some embodiments, the methods described herein can identify a specific subtype of IBD. For example, certain methods can detect that a patient has ulcerative colitis (UC). The patient can then be treated with medications and doses specifically tailored to UC, potentially avoiding medications or doses that are not optimal for treating UC. Another advantage of identifying the subtype of IBD is that it can guide which regions of the gastrointestinal tract are assessed during an endoscopy procedure. For instance, endoscopies for UC often target the large intestine and rectum, whereas endoscopies for CD are often more invasive and may involve parts of the small intestine, such as the ileum. For example, if the methods described herein detect UC in the subject, the subject may undergo an endoscopy focused on the large intestine and rectum, potentially avoiding the more invasive endoscopy typically indicated for CD. The methods provided herein can distinguish UC from CD in a non-surgical way and help patients avoid unnecessary procedures.

[0105] In some embodiments, the methods provided herein can detect the severity of a subtype of IBD (e.g., severe, moderate, mild, or in remission). Understanding the severity of a subtype of IBD is highly valuable for determining an appropriate course of treatment. For example, if a patient is identified as having severe or moderate disease, a clinician may prioritize ordering an endoscopy for further evaluation. Conversely, if the patient is identified as being in remission or having mild disease, the clinician may opt to manage the condition using standard medical care before considering an endoscopy.

[0106] In some embodiments, the methods provided herein can monitor disease progression or assess treatment efficacy in a subject diagnosed with a subtype of IBD. In some embodiments, the methods can inform selection of initial treatment regimen in a treatment-naive subject. In some embodiments, the subject has received a treatment for the subtype of IBD and the methods can inform refinement of this treatment regimen. In some embodiments, the subject may be in remission at the time of sample collection. In some embodiments, the subject may have a flare of worsening symptoms at the time of sample collection. Using a classifier and the cfNA sequencing data, the methods described herein can categorize the severity of the subject’s IBD at the time of sample collection and inform subsequent clinical decisions. For example, if a subject has been on a first medicament at an initial maintenance dose for some time (e.g., about 2-6 weeks), and the subtype of IBD is categorized as being in remission, the current treatment regimen (e.g., amaintenance dose of the medication) should be continued. In some cases, if the classifier categorizes the disease state as in remission, the maintenance dose of the initial medication can also be reduced or discontinued. In this case, a less aggressive treatment may be adopted in the subject in remission. However, if the classifier categorizes the subtype of IBD as mild, moderate, or severe, more aggressive treatments may be recommended based on the severity of the disease. These treatments may include increasing the dose of the initial medication above the maintenance dose, administering a second medication in addition to, or as a replacement for, the initial medication, performing an endoscopic procedure to further evaluate the severity and identify the location of the disease, surgically removing a portion of the GI tract if the endoscopy confirms the presence of moderate or severe IBD, or any combination thereof.

[0107] In some embodiments, the methods provided herein can monitor disease progression or treatment efficacy in a subject having with a subtype of IBD in remission. For example, the methods can analyze a sample comprising cfNA from a subject who has been in remission on a specific IBD treatment over a period of time (e.g., 2-6 weeks). The methods can categorize the severity of the subject’s IBD and inform subsequent clinical decisions. If the subtype of IBD is categorized as being in remission, the current treatment regimen (e.g., a maintenance dose of the initial medication) should be continued. However, if the classifier categorizes the IBD as mild, moderate, or severe, more aggressive treatments may be recommended based on the severity of the disease.In some embodiments, the methods provided herein can monitor the response to surgical intervention in a subject with a subtype of IBD. For example, the methods can analyze a sample from the subject a few weeks (e.g., 2-6 weeks) after the surgical procedure, and the classifier described herein can categorize the severity of the subtype of IBD. If the subtype of IBD is categorized as being in remission, a maintenance therapy can be initiated or continued. If the subtype of IBD is categorized as mild, moderate, or severe, the treatment regimen may be adjusted by modifying either the type of medication or its dosage. Additionally, an endoscopic procedure may be performed to further evaluate the severity of the IBD or to identify the location of the lesions. In some cases, if the endoscopic procedure confirms that the subject is suffering from a moderate or severe subtype of IBD, another surgery may be indicated to remove a portion of the subject’s digestive tract. The methods described herein can ensure ongoing management of the disease based on its progression and response to treatment.Inflammatory disease

[0108] Provided herein, in some embodiments, are methods and compositions for characterization or identification of an inflammatory disease. In some embodiments, detecting or identifying aninflammatory disease comprises identifying an inflammatory disease subtype, or distinguishing between two or more subtypes (e.g., distinguishing between ulcerative colitis (UC) and Crohn’s disease). In some embodiments, detecting or identifying an inflammatory disease comprises identifying a disease severity or distinguishing between two or more disease severities (e.g., between moderate and severe disease or disorder). In some embodiments, identifying an inflammatory disease severity may comprise classifying a disease as mild, moderate, severe, in remission, and / or otherwise healthy, or any combination thereof.

[0109] The methods and compositions provided herein may be applied to one or more inflammatory diseases. In some embodiments, an inflammatory disease disclosed herein is an inflammatory disease that affects the digestive system, gastrointestinal system or tract, or gut, or a combination thereof. In some embodiments, an inflammatory disease (e.g., inflammatory bowel disorder (IBD)) can comprise an inflammatory disease associated with an autoimmune disorder. In some embodiments, an inflammatory disease comprises an inflammatory bowel disease (IBD). In some embodiments, an inflammatory disease may comprise Crohn’s disease, ulcerative colitis, microscopic colitis, autoimmune enteropathy, celiac disease, chronic radiation enteritis, and / or diverticulitis. In some embodiments, IBD may comprise one or more diseases including but not limited to ulcerative colitis (UC), Crohn’ s disease, bowel inflammation, microscopic colitis, and / or indeterminate colitis. In some embodiments, microscopic colitis may comprise lymphocytic colitis. In some embodiments, microscopic colitis may comprise collagenous colitis. In some embodiments, microscopic colitis may comprise lymphocytic colitis and collagenous colitis. In some embodiments, IBD can be associated with inflammation of bowels, inflammation of a colon, or a combination thereof. In some embodiments, IBD may be localized to a single segment of a digestive tract; in some instances, IBD may be present in multiple sites of the digestive tract. In some embodiments, IBD may be present in alternating segments of the digestive tract separated by healthy tissue.

[0110] In some embodiments, Crohn’s disease may affect any part of the gastrointestinal tract. Inflammation in Crohn’s disease can occur in patches, often with healthy tissue between affected areas. In some embodiments, the gastrointestinal tract comprises the mouth and / or the anus. In some embodiments, Crohn’s disease may affect the small bowel, particularly the end of the small bowel (ilium). In some embodiments, Crohn’s disease may affect the end of the small bowel. In some embodiments, Crohn’s disease may affect the colon. In some embodiments, Crohn’s disease may affect the beginning of the colon. In some embodiments, Crohn’s disease may affect the end of the small bowel and the beginning of the colon. In some embodiments, Crohn’s disease may comprise inflammation of the intestinal wall. In some embodiments, Crohn’s disease maycomprise inflammation of one or more layers of the intestinal wall. In some embodiments, Crohn’s disease may comprise inflammation of all layers of the intestinal wall. In some embodiments, ulcerative colitis may affect the colon. In some embodiments, ulcerative colitis may affect the rectum.[oni] In some embodiments, ulcerative colitis may affect the colon and the rectum. In some embodiments, ulcerative colitis may comprise inflammation of the intestinal wall. In some embodiments, ulcerative colitis may comprise inflammation of the large intestine. In some embodiments, ulcerative colitis may comprise inflammation of the superficial lining of the large intestine. In some embodiments, ulcerative colitis may comprise ulcers. In some embodiments, ulcerative colitis may comprise ulcers in the large intestine. In some embodiments, ulcerative colitis may comprise ulcers along the superficial lining of the large intestine. In some embodiments, microscopic colitis may comprise inflammation of the colon. In some embodiments, microscopic colitis may comprise inflammation of the colon that is only visible under a microscope. In some embodiments, diverticulitis may comprise inflammation and / or infection of small pouches (e.g., diverticula) along the walls of the colon. In some embodiments, celiac disease may comprise an autoimmune disorder. In some embodiments, celiac disease may comprise an intolerance to gluten. In some embodiments, celiac disease may comprise an intolerance to gluten which leads to damage of the small intestine. In some embodiments, autoimmune enteropathy may comprise immune-mediated damage of the gastrointestinal tract. In some embodiments, autoimmune enteropathy may comprise severe diarrhea and / or malabsorption. In some embodiments, autoimmune enteropathy may affect the small intestine. In some embodiments, chronic radiation enteritis may comprise chronic inflammation of the bowel. In some embodiments, chronic radiation enteritis may comprise chronic inflammation of the bowel due to previous radiation therapy to the abdomen, pelvis, and / or rectum.

[0112] Provided herein are methods and compositions for identifying a type or subtype of IBD which may affect a particular region of the gastrointestinal tract. In some embodiments, an IBD may affect one or of a colon, a right colon, a transverse colon, an ilium, a small intestine, a large intestine, a stomach, a mouth, a rectum, an anus, an esophagus, a large bowel, and / or a pharynx. In some embodiments, ulcerative colitis may be restricted to the colon. In some embodiments, ulcerative colitis may present with continuous inflammation of the mucosal layer. In some embodiments, Crohn’s disease may affect any part of the gastrointestinal tract. In some embodiments, Crohn’s disease may affect one or more deeper layers of the bowel wall. In some embodiments, Crohn’s disease may affect the large bowel. In some embodiments, Crohn’s disease may affect the small bowel. In some embodiments, Crohn’s disease may affect the large boweland the small bowel. In some embodiments, Crohn’s disease may result in one or more fistulas. In some embodiments, Crohn’s disease may result in one or more strictures. In some embodiments, Crohn’s disease may comprise complications. In some embodiments, complications resulting from Crohn’s disease may comprise one or more fistulas and / or one or more strictures. In some embodiments, Crohn’s disease may require one or more surgical interventions. In some embodiments, complications resulting from Crohn’s disease may require one or more surgical interventions. In some embodiments, ulcerative colitis may require one or more surgical interventions. In some embodiments, a surgical intervention may be curative for ulcerative colitis. In some embodiments, a colectomy may be curative for ulcerative colitis. In some embodiments, a surgical intervention may not be curative for Crohn’s disease. In some embodiments, one or more surgical interventions may be used to manage symptoms of Crohn’s disease. In some embodiments, IBD may comprise extraintestinal manifestations. In some embodiments, ulcerative colitis may comprise extraintestinal manifestations. In some embodiments, Crohn’s disease may comprise extraintestinal manifestations. In some embodiments, extraintestinal manifestations may comprise but are not limited to one or more of arthritis, a skin condition, erythema nodosum, pyoderma gangrenosum, an eye condition, uveitis, episcleritis, a liver condition, a blood vessel condition, joint pain, a skin lesion, inflammation, inflammation of the eye, fatigue, osteoporosis, hepatitis, thrombosis, and any combination thereof. In some embodiments, one or more extraintestinal manifestations of Crohn’s disease may differ from one or more extraintestinal manifestations of ulcerative colitis. In some embodiments, a particular set of one or more extraintestinal manifestations may inform a treatment regimen for an IBD. In some embodiments, Crohn’s disease may comprise arthritis. In some embodiments, Crohn’s disease may comprise one or more skin conditions. In some embodiments, Crohn’s disease may be treated using methotrexate. In some embodiments, Crohn’s disease manifesting with rheumatologic symptoms may be treated using methotrexate.

[0113] In some embodiments, UC is characterized by inflammation of a colon. In some cases, UC is associated with ulcers of the digestive tract. In some embodiments, UC may be confined to the mucosal layer of the colon. In some embodiments, UC may present with continuous inflammation. In some embodiments, UC can affect the large intestine, rectum, colon, or any combination thereof. In some embodiments, UC may result in an increased risk of colorectal cancer. In some embodiments, a total colectomy may be used to treat UC. In some embodiments, a total colectomy may be curative for UC.

[0114] The methods provided herein are particularly useful for detecting a subtype of IBD (e.g., UC or CD) when a subject has indeterminate IBD. Indeterminate colitis can share characteristicsof both UC and Crohn’s Disease (CD) and is generally not distinguishable as either UC or CD using an endoscopy and / or colonoscopy. In some embodiments, the methods and compositions disclosed herein may distinguish a type or subtype of IBD when other diagnostic techniques indicate an IBD is indeterminate. For example, in some cases, an endoscopy may yield indeterminate results. Potential causes of indeterminant results include when a patient has continuous regions of inflammation. Crohn’s disease is associated with patches of inflammation. Severe CD can sometimes present as “continuous” if there is a high density of the CD patches, that makes the patches appear continuous. In such cases, differentiation between CD and UC is difficult. Indeterminant results from an endoscopy can also result when a region of the colon is inaccessible to the endoscope. The region can be inaccessible due to a number of factors including stricture or blockage.

[0115] The methods provided herein are particularly useful for detecting a subtype of IBD (e.g., UC or CD) when a subject has IBD with an unknown subtype. Generally, IBD with an unknown subtype occurs when a clinical evaluation is inconclusive as to whether the subject as UC or CD. This may be, for example, because the subject has symptoms that present both in UC and CD.

[0116] In some embodiments, the methods and compositions disclosed herein may allow for distinguishing between UC and CD without performing a colonoscopy, or in cases of indeterminate colitis. In some embodiments, the methods and compositions disclosed herein may be more effective at differentiating between CD and UC than a colonoscopy. In some embodiments, the methods and compositions disclosed herein may be used to distinguish between a CD and a UC to avoid an incorrect treatment regimen.

[0117] In some embodiments, Crohn’s disease is characterized by inflammation of one or more parts of a digestive tract. In some embodiments, Crohn’s disease may comprise swelling of the bowels. In some embodiments, Crohn’s disease may affect the small intestine, the large intestine, or a combination thereof. In some embodiments, Crohn’s disease may present with transmural inflammation. In some embodiments, Crohn’s disease may affect the entire depth of the intestinal wall. In some embodiments, Crohn’s disease may result in one or more of strictures, fistulas, and abscesses. In some embodiments, Crohn’s disease may result in one or more perianal fistulas. In some embodiments, Crohn’s disease may result in skip lesions. In some embodiments, a skip lesion may comprise areas of disease separated by healthy tissue. In some embodiments, Crohn’s disease may result in an increased risk of colorectal cancer. In some embodiments, a surgery may be used to treat Crohn’s disease. In some embodiments, a surgery may be used to manage symptoms of Crohn’s disease. In some embodiments, Crohn’s disease may recur following a surgery.

[0118] In some embodiments, IBD may comprise an imbalance of one or more strains of bacteria in a digestive tract. In some embodiments, an imbalance of one or more strains of bacteria in a digestive tract may be localized to a segment of the digestive tract. In some embodiments, an imbalance of one or more strains of bacteria in a digestive tract may be localized to multiple segments of the digestive tract.

[0119] In some embodiments, the methods provided herein comprise detecting or diagnosing an inflammatory disease such as IBD, at least in part, based on symptoms, patient presentation, personal medical history, and / or family medical history. In some cases, symptoms and / or patient presentation can be used along with the methods provided herein to detect or diagnose a disease or disorder (e.g., inflammatory disease). In some cases, the methods comprise collecting a sample from a subject or patient with one or more symptoms of IBD and analyzing nucleic acids within the sample (e.g., cfDNA, mcfDNA) to determine whether the symptoms are caused by a particular subtype of inflammatory disease (e.g., a subtype of IBD). In some cases, the methods comprise collecting a sample from a subject or patient with one or more symptoms of IBD and analyzing nucleic acids within the sample (e.g., cfDNA, mcfDNA) to determine whether the symptoms are associated with a certain severity of inflammatory disease (e.g., IBD, a subtype of IBD).

[0120] In some embodiments, an IBD may be diagnosed via a physical examination, blood test, stool test, imaging study, reported symptoms, medications, personal medical history, family medical history, or any combination thereof. In some embodiments, symptoms of IBD may include but are not limited to: pain, discomfort, cramps, diarrhea, blood in the stool, mucus in the stool, stool urgency, weight loss, fever, poor appetite, mouth sores, low blood count, iron deficiency anemia, fatigue, joint pain, rashes, swelling, kidney stones, dehydration, malnutrition, bowel blockage, fistula, vomiting, colon cancer, rectal cancer, reduced bone density, eye irritation, skin changes, inflammation, inflammation of the skin, inflammation of the eye, inflammation of the joints, inflammation of the liver, inflammation of the bile ducts, delayed and / or impaired growth (in children), depression, anxiety, distress, mental health disturbance, and / or disruptions in daily functioning, or any combination thereof. In some embodiments, symptoms of Crohn’s disease may include but are not limited to: abdominal pain, diarrhea, weight loss, fatigue, fever, blood in stool, reduced appetite, nausea, bloating, joint pain, skin rashes, and / or mouth sores, or any combination thereof. In some embodiments, symptoms of ulcerative colitis may include but are not limited to: abdominal pain, diarrhea (often with blood), fatigue, weight loss, urgency to have bowel movements, rectal bleeding, fever, nausea, loss of appetite, and / or anemia, or any combination thereof. In some embodiments, symptoms of an inflammatory bowel condition may include but are not limited to one or more of: long-term inflammation of the digestive tract, digestivediscomfort, stomach cramps and pain, diarrhea, constipation, urgent need to have a bowel movement, feeling as though a bowel movement was incomplete, rectal bleeding, loss of appetite, weight loss, fatigue, night sweats, irregular periods, or any combination thereof.

[0121] In some embodiments, IBD may have a genetic component. In some embodiments, IBD may comprise cell death in the intestinal tract. In some embodiments, IBD may comprise release of cell-free DNA into the bloodstream at the intestinal tract. In some embodiments, Crohn’s disease may have a genetic component. In some embodiments, ulcerative colitis may have a genetic component.

[0122] In some embodiments, IBD in a subject may be classified as mild, moderate, severe, or in remission. In some embodiments, ulcerative colitis in a subject may be classified as mild, moderate, severe, or in remission, or otherwise healthy, or any combination thereof. In some embodiments, mild ulcerative colitis may comprise fewer than four rectal bleeding episodes per day. In some embodiments, moderate ulcerative colitis may comprise more than four rectal bleeding episodes per day. In some embodiments, severe ulcerative colitis may comprise more than four rectal bleeding episodes per day. In some embodiments, severe ulcerative colitis may comprise more than four rectal bleeding episodes per day in addition to one or more systemic symptoms including but not limited to fever and anemia. In some embodiments, UC may start with mild symptoms and gradually worsen.

[0123] In some embodiments, Crohn’s disease in a subject may be classified as mild, moderate, severe, or in remission. In some embodiments, mild Crohn’s disease may comprise abdominal pain and / or diarrhea. In some embodiments, moderate Crohn’s disease may comprise abdominal pain, diarrhea, weight loss, and / or nutritional deficiency. In some embodiments, severe Crohn’s disease may comprise abdominal pain, diarrhea, weight loss, nutritional deficiency, one or more intestinal obstructions, and / or limited daily function. In some embodiments, Crohn’s disease may be progressive. In some embodiments, Crohn’s disease may start with mild symptoms and gradually worsen.

[0124] Provided herein are methods and compositions for distinguishing between types or subtypes of inflammatory disease. In some embodiments, distinguishing an inflammatory disease may comprise distinguishing between subtypes of disease that have one or more overlapping symptoms. In some embodiments, distinguishing between subtypes of disease may comprise distinguishing between inflammatory bowel disorder and a healthy state. In some embodiments, distinguishing between subtypes of disease may comprise distinguishing between inflammatory bowel disorder and a state of remission. In some embodiments, distinguishing between subtypes of disease may comprise distinguishing between Crohn’s disease and ulcerative colitis. In someembodiments, distinguishing between subtypes of disease may comprise distinguishing between Crohn’s disease and a state of remission. In some embodiments, distinguishing between subtypes of disease may comprise distinguishing between Crohn’s disease and a healthy state. In some embodiments, distinguishing between subtypes of disease may comprise distinguishing between ulcerative colitis and a state of remission. In some embodiments, distinguishing between subtypes of disease may comprise distinguishing between ulcerative colitis and a healthy state.

[0125] In some embodiments, identifying or detecting an inflammatory disease may comprise distinguishing between one or more severity levels of a disease. In some embodiments, a severity level of a disease may comprise a diagnosed severity. In some embodiments, a diagnosed severity may comprise a diagnosed severity based on patient symptoms. In some embodiments, severity of a disease may change over time. In some embodiments, severity of a disease may increase over time. In some embodiments, severity of a disease may decrease over time. In some embodiments, severity of a disease may remain the same over time. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a severe disease, a moderate disease, a mild disease, a disease in remission, and a healthy state. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a severe disease, a moderate disease, a mild disease, and a disease in remission. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a severe disease, a moderate disease, and a mild disease. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a severe disease and a moderate disease. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a severe disease and a mild disease. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a moderate disease and a mild disease. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a severe disease and a disease in remission. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a moderate disease and a disease in remission. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a mild disease and a disease in remission. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a moderate disease and a healthy state. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a mild disease and a healthy state. In some embodiments, distinguishing between one or more severity levels of a disease may comprisedistinguishing between a severe disease and a healthy state. In some embodiments, distinguishing between one or more severity levels of a disease may comprise distinguishing between a disease in remission and a healthy state.

[0126] Provided herein are methods and compositions for distinguishing one or more severity levels of an inflammatory disease. In some embodiments, a severity level of an IBD may be determined according to a scoring tool. In some embodiments, a severity level of Crohn’s disease may be determined according to a scoring tool. In some embodiments, a severity level of ulcerative colitis may be determined according to a scoring tool. In some embodiments, a Simplified Endoscopic Score for Crohn’s Disease (SES-CD) may be used to determine a severity level of Crohn’s disease. In some embodiments, an SES-CD may comprise findings obtained via endoscopy. In some embodiments, an SES-CD may comprise findings obtained via endoscopic observation of intestinal mucosa. In some embodiments, an SES-CD may be used in clinical practice. In some embodiments, an SES-CD may be used to assess disease activity. In some embodiments, an SES-CD may be used to assess response to treatment. In some embodiments, an SES-CD may be used to assess disease progression. In some embodiments, an SES-CD may assess one or more of the following segments of bowel: ileum, right colon, transverse colon, and / or left colon / sigmoid.

[0127] In some embodiments, an SES-CD may comprise the following scoring:1. Size of Ulcers: The size of ulcers is scored as follows:1. 0: No ulcers2. 1 : Aphthous ulcers3. 2: Large ulcers (larger than aphthous)4. 3: Very large ulcers, confluent, or with a diameter >1 cm2. Ulcerated Surface:1. 0: No ulcerated surface2. 1 : < 10% ulcerated3. 2: 10-30% ulcerated4. 3: >30% ulcerated3. Affected Surface:1. 0: No affected surface2. 1 : <50% affected surface3. 2: 50-75% affected surface4. 3: >75% affected surface4. Stenosis:1. 0: No stenosis2. 1 : Single, passable with the endoscope3. 2: Multiple stenoses, but passable with the endoscope4. 3 : Not passable with the endoscope

[0128] In some embodiments, an SES-CD may comprise scoring four parameters. In some embodiments, the four parameters of an SES-CD may comprise size of ulcers, ulcerated surface, affected surface, and stenosis. In some embodiments, an SES-CD may comprise scoring four parameters separately. In some embodiments, an SES-CD may comprise scoring four parameters separately for each segment of bowel. In some embodiments, scores of separate parameters evaluated in an SES-CD may be added together across all segments. In some embodiments, a total score may be calculated in an SES-CD. In some embodiments, a total score calculated in an SES- CD may comprise the sum of scores obtained for four parameters as described herein across all examined segments. In some embodiments, an SES-CD total score may comprise a minimum total score of 0. In some embodiments, an SES-CD total score of 0 may indicate no disease activity. In some embodiments, an SES-CD total score may comprise a value of from 0 to 12. In some embodiments, an SES-CD total score may comprise 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12. In some embodiments, an SES-CD may be used to guide therapeutic decisions. In some embodiments, an SES-CD may be used to monitor disease progression. In some embodiments, an SES-CD may be used to monitor disease remission in response to treatment.

[0129] In some embodiments, a Mayo Endoscopic Score may be used to determine an inflammation severity of a disease. In some embodiments, a Mayo Endoscopic Score may comprise four categories of severity. In some embodiments, a Mayo Endoscopic Score may be determined via endoscopy. In some embodiments, each category of a Mayo Endoscopic Score may be assigned according to worst affected area observed during an endoscopy. In some embodiments, a Mayo Endoscopic Score may provide a visual-based assessment of inflammation severity. In some embodiments, a Mayo Endoscopic Score may be used to determine extent of disease activity. In some embodiments, a Mayo Endoscopic Score may be used to guide one or more treatment decisions. In some embodiments, a Mayo Endoscopic Score may be used to evaluate a response to a therapy. In some embodiments, a Mayo Endoscopic Score may comprise a score of 0, 1, 2, or 3.

[0130] In some embodiments, a Mayo Endoscopic Score may comprise the following scoring:1. 0 (Normal): No signs of inflammation.2. 1 (Mild disease): Mild inflammation with slight erythema (redness), decreased vascular pattern, and no bleeding.3. 2 (Moderate disease): Moderate inflammation with marked erythema, absent vascular patterns, friability (tissue that bleeds upon slight manipulation), and erosions.4. 3 (Severe disease): Severe inflammation with spontaneous bleeding, ulcers, or both.

[0131] In some embodiments, distinguishing an inflammatory disease may comprise distinguishing between one or more severity levels of a disease. In some embodiments, distinguishing an inflammatory disease may comprise distinguishing between one or more severity levels of an ulcerative colitis. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a severe ulcerative colitis, a moderate ulcerative colitis, a mild ulcerative colitis, an ulcerative colitis in remission, and a healthy state. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a severe ulcerative colitis, a moderate ulcerative colitis, a mild ulcerative colitis, and an ulcerative colitis in remission. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a severe ulcerative colitis, a moderate ulcerative colitis, and a mild ulcerative colitis. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a severe ulcerative colitis and a moderate ulcerative colitis. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a severe ulcerative colitis and a mild ulcerative colitis. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a moderate ulcerative colitis and a mild ulcerative colitis. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a severe ulcerative colitis and an ulcerative colitis in remission. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a moderate ulcerative colitis and an ulcerative colitis in remission. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a mild ulcerative colitis and an ulcerative colitis in remission. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a moderate ulcerative colitis and a healthy state. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a mild ulcerative colitis and a healthy state. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between a severe ulcerative colitis and a healthy state. In some embodiments, distinguishing between one or more severity levels of an ulcerative colitis may comprise distinguishing between an ulcerative colitis in remission and a healthy state.

[0132] In some embodiments, distinguishing an inflammatory disease may comprise distinguishing between one or more severity levels of a disease. In some embodiments, distinguishing an inflammatory disease may comprise distinguishing between one or more severity levels of a Crohn’s disease. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a severe Crohn’s disease, a moderate Crohn’s disease, a mild Crohn’s disease, a Crohn’s disease in remission, and a healthy state. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a severe Crohn’s disease, a moderate Crohn’s disease, a mild Crohn’s disease, and a Crohn’s disease in remission. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a severe Crohn’s disease, a moderate Crohn’s disease, and a mild Crohn’s disease. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a severe Crohn’s disease and a moderate Crohn’s disease. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a severe Crohn’s disease and a mild Crohn’s disease. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a moderate Crohn’s disease and a mild Crohn’s disease. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a severe Crohn’s disease and a Crohn’s disease in remission. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a moderate Crohn’s disease and a Crohn’s disease in remission. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a mild Crohn’s disease and a Crohn’s disease in remission. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a moderate Crohn’s disease and a healthy state. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a mild Crohn’ s disease and a healthy state. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a severe Crohn’s disease and a healthy state. In some embodiments, distinguishing between one or more severity levels of a Crohn’s disease may comprise distinguishing between a Crohn’s disease in remission and a healthy state.Physical enrichment of nucleic acids in inflammatory disease

[0133] Disclosed herein are methods and compositions for enrichment of cell-free DNA or RNA from a sample derived from a subject diagnosed with, or suspected of having, an inflammatorydisease. In some embodiments, the methods disclosed herein may be applied to non-cell-free DNA or RNA. In some embodiments, enrichment may comprise physical enrichment. As used herein, the terms “physical enrichment”, or “physically enriched” can refer to a method by which nucleic acids are separated, filtered, amplified, or otherwise selected for a characteristic. In some embodiments, a characteristic can comprise a size, a length, a sequence, a physical modification (such as, but not limited to, phosphorylation, methylation, etc.), a strandedness, and / or a species. In some embodiments, a strandedness can comprise a sing-strandedness or a double-strandedness. In some embodiments, physically enriching can comprise increasing a percentage of nucleic acids within a plurality of nucleic acids that contain a characteristic.

[0134] In some embodiments, cell-free DNA in a sample may be physically enriched before sequencing. In some embodiments, cell-free DNA in a sample may be computationally enriched after sequencing. In some embodiments, cell-free DNA in a sample may not be enriched before sequencing. In some embodiments, cell-free DNA in a sample may not be enriched after sequencing. In some embodiments, cell-free DNA in a sample may not be enriched before or after sequencing. In some embodiments, cell-free DNA may be physically enriched for cell-free DNA fragments of a certain size and / or a range of sizes. In some embodiments, cell-free DNA may be physically enriched for cell-free DNA fragments of a certain size, or range of sizes, to distinguish between subtypes of IBD and / or to distinguish between severity of IBD. In some embodiments, the methods comprise enriching for mcfDNA in a sample comprising human and mcfDNA to distinguish between subtypes of IBD and / or to distinguish between severity of IBD. In some embodiments, enriching for mcfDNA may comprising physically enriching for a particular size or length value to distinguish between subtypes of IBD and / or to distinguish between severity of IBD. In some embodiments, the methods comprise enriching for human cfDNA in a sample comprising human and mcfDNA to distinguish between subtypes of IBD and / or to distinguish between severity of IBD. In some embodiments, enriching for human cfDNA may comprising physically enriching for human cfDNA of a particular size or length value. In some embodiments, cell-free DNA may be physically enriched for cell-free DNA fragments of a certain size or range of sizes. In some embodiments, cell-free DNA may be physically enriched for cell-free DNA fragments of a certain size prior to sequencing. In some embodiments, physically enriching for cell-free DNA fragments of a certain size may increase the analytical power of an assay. In some embodiments, physically enriching for cell-free DNA fragments of a certain size may be critical to detecting or identifying a disease and / or a disease severity in a subject.

[0135] In some embodiments, physically enriching for cell-free DNA fragments of a certain size may comprise enriching for fragments of a certain length meeting a cutoff value. In someembodiments, a cutoff value may encompass a range of values. In some embodiments, a cutoff value may encompass any of the values between a range of values. As used herein, in some embodiments, if a range for enrichment has an upper cutoff value of, for example, 50-150 bases and a lower cutoff value of, for example, 5-10 bases, then this range can include physical enrichment ranges such as 5-100 bases, 6-120 bases, 8-75 bases, etc. In some embodiments, physically enriching for less than 100 bases includes a method that physically enriches for less than 60 bases. In some embodiments, a cutoff value may encompass a range of base pair lengths. In some embodiments, a cutoff value may encompass an upper limit. In some embodiments, a cutoff value may encompass a lower limit. In some embodiments, a cutoff value may encompass an upper limit and a lower limit.

[0136] In some embodiments, an upper limit and / or a lower limit may comprise a direct limit according to a physical technique. In some embodiments, a direct limit according to a physical technique may comprise using gel-electrophoresis to remove fragments below and / or above a set length. In some embodiments, an indirect limit according to a physical technique may comprise using a technique that has a tendency for enriching for a particular size. In some cases, using beadbased size selection to physically enrich for an approximate fragment size can be an indirect technique. In some embodiments, bead-based size selection may comprise a solid support capable of separating cell-free nucleic acids based on size. In some embodiments, bead-based size selection may comprise eluting cell-free nucleic acids from a solid support. In some cases, the solid support comprises beads; in some cases, a solid support can comprise magnetic beads.

[0137] In some embodiments, cell-free DNA fragments may be physically enriched for cell-free DNA fragments that are greater than 5 bp, greater than 10 bp, greater than 15 bp, greater than 20 bp, greater than 25 bp, greater than 30 bp, greater than 35 bp, greater than 40 bp, greater than 45 bp, or greater than 50 bp in length. In some embodiments, cell-free DNA fragments may be physically enriched for cell-free DNA fragments that are less than 200 bp, less than 190 bp, less than 180 bp, less than 170 bp, less than 160 bp, less than 150 bp, less than 140 bp, less than 130 bp, less than 120 bp, less than 110 bp, less than 100 bp, less than 90 bp, less than 80 bp, less than 70 bp, less than 60 bp, less than 50, less than 40 bp in length, less than 30 bp in length, less than 20 bp in length, or less than 10 bp in length. In some embodiments, cell-free DNA fragments may be physically enriched for cell-free DNA fragments that are about 200 bp, about 190 bp, about 180 bp, about 170 bp, about 160 bp, about 150 bp, about 140 bp, about 130 bp, about 120 bp, about 110 bp, about 100 bp, about 90 bp, about 80 bp, about 70 bp, about 60 bp, about 50 bp, about 40 bp in length, about 30 bp in length, about 20 bp in length, or about 10 bp in length. In some embodiments, microbial cell-free DNA fragments may be physically enriched for microbial cell-free DNA fragments that are greater than 5 bp, greater than 10 bp, greater than 15 bp, greater than 20 bp, greater than 25 bp, greater than 30 bp, greater than 35 bp, greater than 40 bp, greater than 45 bp, or greater than 50 bp in length. In some embodiments, sequence reads generated from microbial cell-free DNA may be physically enriched for microbial cell-free DNA fragments that are less than 200 bp, less than 190 bp, less than 180 bp, less than 170 bp, less than 160 bp, less than 150 bp, less than 140 bp, less than 130 bp, less than 120 bp, less than 110 bp, less than 100 bp, less than 90 bp, less than 80 bp, less than 70 bp, less than 60 bp, less than 50, less than 40 bp in length, less than 30 bp in length, less than 20 bp in length, or less than 10 bp in length. In some embodiments, sequence reads generated from microbial cell-free DNA may be physically enriched for fragments that are about 200 bp, about 190 bp, about 180 bp, about 170 bp, about 160 bp, about 150 bp, about 140 bp, about 130 bp, about 120 bp, about 110 bp, about 100 bp, about 90 bp, about 80 bp, about 70 bp, about 60 bp, about 50 bp, about 40 bp in length, about 30 bp in length, about 20 bp in length, or about 10 bp in length. In some embodiments, subject cell-free DNA fragments may be physically enriched for subject cell-free DNA fragments that are greater than 5 bp, greater than 10 bp, greater than 15 bp, greater than 20 bp, greater than 25 bp, greater than 30 bp, greater than 35 bp, greater than 40 bp, greater than 45 bp, or greater than 50 bp in length. In some embodiments, sequence reads generated from subject cell-free DNA may be physically enriched for fragments that are less than 200 bp, less than 190 bp, less than 180 bp, less than 170 bp, less than 160 bp, less than 150 bp, less than 140 bp, less than 130 bp, less than 120 bp, less than 110 bp, less than 100 bp, less than 90 bp, less than 80 bp, less than 70 bp, less than 60 bp, less than 50, less than 40 bp in length, less than 30 bp in length, less than 20 bp in length, or less than 10 bp in length. In some embodiments, sequence reads generated from subject cell-free DNA may be physically enriched for fragments that are about 200 bp, about 190 bp, about 180 bp, about 170 bp, about 160 bp, about 150 bp, about 140 bp, about 130 bp, about 120 bp, about 110 bp, about 100 bp, about 90 bp, about 80 bp, about 70 bp, about 60 bp, about 50 bp, about 40 bp in length, about 30 bp in length, about 20 bp in length, or about 10 bp in length. In some embodiments, cell- free DNA fragments may be physically enriched for cell-free DNA fragments that are 10 - 200 bp in length. In some embodiments, cell-free DNA fragments may be physically enriched for cell- free DNA fragments that are 50 - 200 bp in length. In some embodiments, cell-free DNA fragments may be physically enriched for cell-free DNA fragments that are 10 - 100 bp in length. In some embodiments, cell-free DNA fragments may be physically enriched for cell-free DNA fragments that are 50 - 150 bp in length. In some embodiments, cell-free DNA fragments may be physically enriched for cell-free DNA fragments that are 150 - 200 bp in length. In some embodiments, cell-free DNA fragments may be physically enriched for cell-free DNA fragmentsthat are less than 170 bp in length. In some embodiments, any of the lengths disclosed herein may comprise native DNA. In some embodiments, any of the lengths disclosed herein may comprise native DNA and one or more adapters. In some embodiments, DNA may be physically enriched for single-stranded DNA (ssDNA). In some embodiments, DNA may be physically enriched for ssDNA of a particular length of any of the lengths disclosed herein. In some embodiments, DNA may be physically enriched for double-stranded DNA (dsDNA). In some embodiments, DNA may be physically enriched for dsDNA of a particular length of any of the lengths disclosed herein.

[0138] In some embodiments, enrichment of cell-free DNA fragments may comprise bead-based size selection. In some embodiments, enrichment of cell-free DNA fragments may comprise the use of a solvent, for example, an acetate, alcohol, such as methanol, ethanol, or isopropanol. In some embodiments, enrichment of cell-free DNA fragments (e.g., mcfDNA or relatively short human or host cfDNA) may comprise size selection electrophoresis (e.g., gel-electrophoresis). In some embodiments, enrichment of microbial cell-free DNA fragments (and. or human cfDNA fragments) may comprise use of size-selection electrophoresis (e.g., gel-electrophoresis). In some embodiments, enrichment may comprise contacting a sample with a solid support (e.g., beads) to separate nucleic acids based on size or length. In some embodiments, enrichment may comprise contacting a solid support (e.g., beads) with a solution comprising solvent, for example, an acetate, alcohol, such as methanol, ethanol, or isopropanol, such as after nucleic acids within a sample are bound to the solid support. In some embodiments, enrichment may comprise the use of binding buffer. In some embodiments, sequence reads generated from microbial cell-free DNA may be physically enriched for short fragments. In some embodiments, sequence reads generated from microbial cell-free DNA may be physically enriched for ultra-degraded fragments. In some embodiments, physical enrichment may comprise bead-based size selection. In some embodiments, physical enrichment of subject cell-free DNA fragments may comprise gelelectrophoresis. In some embodiments, physical enrichment may comprise the use of a solvent, for example, an acetate, alcohol, such as methanol, ethanol, or isopropanol. In some embodiments, physical enrichment may comprise the use of binding buffer. In some embodiments, relative enrichment or relative depletion of microbial cell-free DNA may be detected, calculated, or a combination thereof after physical enrichment of the microbial cell-free DNA. In some embodiments, relative enrichment or relative depletion of subject cell-free DNA may be detected, calculated, or a combination thereof after physical enrichment of the subject cell-free DNA.Sequencing of cell-free nucleic acids in inflammatory disease

[0139] Provided herein are methods and compositions for sequencing of cell-free DNA derived from a subject diagnosed with an inflammatory disease. In some embodiments, cell-free DNAfragments are sequenced following enrichment. In some embodiments, sequencing may comprise high throughput sequencing. In some embodiments, sequencing may comprise massively parallel sequencing, Next Generation sequencing, and / or post-Next Generation sequencing. In some embodiments, cell-free DNA fragments are sequenced via deep sequencing. In some embodiments, cell-free DNA fragments are sequenced using ultra deep sequencing. In some embodiments, sequencing cell-free DNA fragments may comprise sequencing from 100 million to 200 million reads per sample of cell-free DNA fragments. In some embodiments, ultra deep sequencing of cell-free DNA fragments may comprise sequencing from 100 million to 200 million reads per sample of cell-free DNA fragments. In some embodiments, sequencing cell-free DNA fragments may comprise sequencing from 100 million to 300 million reads per sample of cell-free DNA fragments. In some embodiments, ultra deep sequencing of cell-free DNA fragments may comprise sequencing from 200 million to 300 million reads per sample of cell-free DNA fragments. In some embodiments, sequencing cell-free DNA fragments may comprise sequencing from 200 million to 400 million reads per sample of cell-free DNA fragments. In some embodiments, ultra deep sequencing of cell-free DNA fragments may comprise sequencing from 200 million to 400 million reads per sample of cell-free DNA fragments. In some embodiments, sequencing cell-free DNA fragments may comprise sequencing from 300 million to 400 million reads per sample of cell-free DNA fragments. In some embodiments, ultra deep sequencing of cell-free DNA fragments may comprise sequencing from 300 million to 400 million reads per sample of cell-free DNA fragments. In some embodiments, ultra deep sequencing of cell-free DNA fragments may comprise sequencing greater than 100 million, 200 million, 300 million, 400 million, 500 million, 600 million, 700 million, or 800 million reads per sample of cell-free DNA fragments. In some embodiments, cell-free DNA fragments can be sequenced using 10-20 million, 20-50 million, or 50-100 million reads per sample. In some embodiments, cell-free DNA fragments can be sequenced at an average depth of about 5-10, about 10-20, about 20-30, about 30-40, about 40-50, or about 50-100 reads per base.

[0140] In some embodiments, sequencing of cell-free DNA fragments may comprise 5X coverage per base pair. In some embodiments, sequencing of cell-free DNA fragments may comprise 10X coverage per base pair. In some embodiments, sequencing of cell-free DNA fragments may comprise 15X coverage per base pair. In some embodiments, sequencing of cell-free DNA fragments may comprise 5X, 10X, 15X, 20X, 25X, 30X, 35X, 40X, 45X, 50X, 55X, 60X, 65X, 70X, 75X, 80X, 85X, 90X, 95X, or 100X coverage per base pair. In some embodiments, sequencing of cell-free DNA fragments may comprise at least 2X, 3X, 4X, 5X, 6X. 7X, 8X, 9X, 10X, 15X, 20X, 25X, 30X, 35X, 40X, 45X, 50X, 55X, 60X, 65X, 70X, 75X, 80X, 85X, 90X, 95X,or 100X coverage per base pair. In some embodiments, sequencing of cell-free DNA fragments may comprise at most 8X, 9X, 10X, 15X, 20X, 25X, 30X, 35X, 40X, 45X, 50X, 55X, 60X, 65X, 70X, 75X, 80X, 85X, 90X, 95X, or 100X coverage per base pair.

[0141] In some embodiments, one or more samples of cell-free DNA fragments may be grouped for sequencing. In some embodiments, sequencing of cell-free DNA fragments may comprise Illumina® sequencing. In some embodiments, one or more samples of cell-free DNA fragments may be grouped for sequencing on an Illumina® 6000 S4 flowcell. In some embodiments, at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 samples of cell-free DNA fragments may be grouped for sequencing. In some embodiments, sequencing of cell-free DNA fragments may generate at least 100 million, at least 150 million, at least 200 million, at least 250 million, at least 300 million, at least 350 million, at least 400 million, at least 450 million, or at least 500 million paired-end reads per dataset.Detecting or identifying relative enrichment and / or relative depletion of cell-free DNA at a locus

[0142] Provided herein are methods and compositions for determining relative enrichment and / or relative depletion of cell-free DNA at a genetic locus relative to genomic regions flanking that locus. In some embodiments, a genetic locus can comprise a microbial genetic locus. In some embodiments, a locus can comprise a human genetic locus. In some embodiments, a genetic locus can comprise one or more regions of DNA in a genome. In some embodiments, a genetic locus may comprise a genomic locus. In some embodiments, a genome may comprise a human genome. In some embodiments, a genome may comprise a microbial genome. In some embodiments, detecting or identifying relative enrichment and / or relative depletion of cell-free DNA may comprise identifying one or more relatively enriched and / or relatively depleted promoters. In some embodiments, detecting or identifying relatively enriched and / or relatively depleted cell-free DNA may comprise identifying one or more relatively enriched and / or relatively depleted transcription start sites (TSSs). In some embodiments, detecting or identifying relatively enriched and / or relatively depleted cell-free DNA may comprise generating sequence reads from the cell-free DNA.

[0143] In some embodiments, determining that a genetic locus is relatively enriched and / or relatively depleted may comprise determining a natural log ratio of a number of sequence reads. In some embodiments, determining a natural log ratio of a number of sequence reads may comprise determining a natural log ratio of a number of sequence reads covering a region within 500 bp of a genetic locus to a number of sequence reads located more than 500 bp but within 2000 bp in either the 5’ direction or the 3’ direction from the genetic locus. In some embodiments, determininga natural log ratio of a number of sequence reads may comprise determining a natural log ratio of a number of sequence reads covering a region within 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, or 600 bp of a genetic locus to a number of sequence reads located more than 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, or 600 bp, but within 500, 1000, 1500, 2000, or 2500 bp in either the 5’ direction or the 3’ direction from the genetic locus. In some embodiments, detecting or identifying relatively enriched cell-free DNA may comprise calculating a peak-to- flank natural log ratio. In some embodiments, detecting or identifying relatively depleted cell-free DNA may comprise calculating a trough-to-flank natural log ratio. In some embodiments, a peak- to-flank natural log ratio can have a value of 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1, or greater. In some embodiments, a trough-to-flank natural log ratio can have a value of -0.1, -0.15, -0.2, -0.25, -0.3, -0.35, -0.4, -0.45, -0.5, -0.55, -0.6, -0.65, -0.7, -0.75, -0.8, -0.85, -0.9, -0.95, -1, or less. In some embodiments, a natural log ratio of sequence reads may indicate a relative enrichment at a given genetic locus. In some embodiments, a natural log ratio of sequence reads may indicate a relative depletion at a given genetic locus. In some embodiments, an absolute value of a peak-to-flank natural log ratio or of a trough-to-flank natural log ratio of 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1, or greater may indicate a relative enrichment of a genetic locus. In some embodiments, a peak-to-flank natural log ratio of 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1, or greater may indicate a relative enrichment of a genetic locus. In some embodiments, an absolute value of a trough-to-flank natural log ratio or of a trough-to-flank natural log ratio of -0.1, -0.15, -0.2, -0.25, -0.3, -0.35, -0.4, -0.45, -0.5, -0.55, -0.6, -0.65, -0.7, - 0.75, -0.8, -0.85, -0.9, -0.95, -1, or less may indicate a relative depletion of a genetic locus. In some embodiments, a trough-to-flank natural log ratio of -0.1, -0.15, -0.2, -0.25, -0.3, -0.35, -0.4, -0.45, -0.5, -0.55, -0.6, -0.65, -0.7, -0.75, -0.8, -0.85, -0.9, -0.95, -1, or less may indicate a relative depletion of a genetic locus.

[0144] In some embodiments, one or more relatively enriched and / or relatively depleted genomic loci may constitute a signature. In some embodiments, a signature may indicate a presence of an inflammatory disorder. In some embodiments, a signature may indicate a presence of an inflammatory bowel disorder. In some embodiments, a signature may indicate a presence of ulcerative colitis. In some embodiments, a signature may indicate a presence of Crohn’s disease. In some embodiments, a signature may indicate a disease severity. In some embodiments, a signature may indicate a mild, moderate, or severe disease severity or a disease in remission.

[0145] Disclosed herein in some embodiments is a method of use of plasma cell-free DNA (cfDNA) as a means to assess inflammatory bowel disease type and severity. In someembodiments, subject cell-free DNA may be sequenced to generate sequence reads. In some embodiments, sequence reads generated from subject cell-free DNA may be mapped onto one or more reference genomes. In some embodiments, sequence reads generated from subject cell-free DNA may be analyzed to identify one or more relatively enriched or relatively depleted promoters. In some embodiments, sequence reads generated from subject cell-free DNA may be analyzed to identify one or more relatively enriched or relatively depleted regulatory elements. In some embodiments, sequence reads generated from subject cell-free DNA may be analyzed to identify one or more relatively enriched or relatively depleted transcription start sites (TSSs). In some embodiments, sequence reads generated from subject cell-free DNA may be analyzed to identify one or more relatively enriched or relatively depleted genes. In some embodiments, sequence reads generated from subject cell-free DNA may be analyzed via paired-end sequencing. In some embodiments, paired-end alignments may be generated from subject cell-free DNA sequence reads. In some embodiments, analysis of paired-end alignments may be used to identify one or more relatively enriched or relatively depleted genes. In some embodiments, one or more relatively enriched or relatively depleted genes may comprise one or more gene-specific biomarkers. In some embodiments, gene-specific biomarkers may be computed using one or more fragmentomic-based algorithms. In some embodiments, one or more fragmentomic-based algorithms may comprise for example refTSS and / or ENCODE. In some embodiments, additional analysis of data obtained from processing of nucleic acids as described herein may be performed using machine learning. In some embodiments, machine learning may comprise the use of a machine-learning classifier. In some embodiments, a machine-learning classifier is also known as a trained algorithm. In some embodiments, performance of a machine-learning classifier as disclosed herein may be assessed using a 10-fold cross-validation. In some embodiments, a 10-fold cross-validation may be performed multiple times across different partitions. In some embodiments, a 10-fold cross- validation may comprise a leave one clinical site out (LOSO) strategy. In some embodiments, a machine-learning classifier may comprise a generative model.Detecting or identifying relatively enriched or depleted genes or promoters to detect or identify disease

[0146] Provided herein are methods and compositions for identifying one or more genes and / or promoters relatively enriched or relatively depleted in a patient sample for a patient who has a disease as compared to a healthy control. In some embodiments, one or more genes may be analyzed to determine a type and / or severity of an inflammatory bowel disorder in a patient. In some embodiments, a patient may be a human patient. In some embodiments, a patient may be healthy. In some embodiments, a patient may have a disease in remission. In some embodiments,a patient may have a disease. In some embodiments, a patient may have an inflammatory disorder. In some embodiments, a patient may have an autoimmune condition. In some embodiments, a patient may have an inflammatory bowel disorder. In some embodiments, an inflammatory bowel disorder may comprise ulcerative colitis. In some embodiments, an inflammatory bowel disorder may comprise Crohn’s disease.

[0147] In some embodiments, one or more genes listed in Table 2 may be analyzed to determine a type and / or severity of an inflammatory bowel disorder. In some embodiments, at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, at least twenty, at least twenty-one, at least twenty -two, at least twenty -three, at least twenty -four, at least twenty -five, at least twenty-six, at least twenty-seven, at least twenty-eight, at least twenty-nine, at least thirty, at least thirty-one, at least thirty-two, at least thirty-three, at least thirty-four, at least thirty-five, at least thirty-six, at least thirty-seven, at least thirty-eight, at least thirty -nine, at least forty, at least forty-one, at least forty -two, at least forty -three, at least forty-four, at least forty -five, at least forty- six, at least forty-seven, at least forty-eight, at least forty-nine, at least fifty, at least fifty-one, at least fifty-two, at least fifty-three, at least fifty-four, at least fifty-five, at least fifty-six, at least fifty-seven, at least fifty-eight, at least fifty-nine, at least sixty, at least sixty-one, at least sixty- two, at least sixty -three, at least sixty-four, at least sixty-five, at least sixty-six, at least sixty-seven, at least sixty-eight, at least sixty-nine, at least seventy, at least seventy-one, at least seventy-two, at least seventy-three, at least seventy-four, at least seventy-five, at least seventy-six, at least seventy-seven, at least seventy-eight, at least seventy-nine, at least eighty, at least eighty-one, at least eighty-two, at least eighty-three, at least eighty-four, at least eighty-five, at least eighty-six, at least eighty-seven, at least eighty-eight, at least eighty-nine, at least ninety, at least ninety-one, at least ninety-two, at least ninety-three, at least ninety-four, at least ninety-five, at least ninety- six, at least ninety-seven, at least ninety-eight, at least ninety-nine, or at least one hundred genes listed in Table 2 may be analyzed to determine a type and / or severity of an inflammatory bowel disorder. In some embodiments, one or more of the following genes may be analyzed to determine a type and / or severity of an inflammatory bowel disorder: 'C3', 'SNURF, 'SNRPN', 'ACE2', 'TMEM259', 'FANCF', 'C21orf62-ASl', 'STXBP1', 'ZCCHC10', and / or 'ZNF148'. In some embodiments, one or more of the following genes may be analyzed to determine a type and / or severity of an inflammatory bowel disorder: 'GPIHBP1', 'PAXBP1', 'AIFl', 'POFUT2', 'SCAT1', 'LINC00205', 'MMGT1', 'SIGLEC15', 'SNAPC4', and / or 'LINC01970'. In some embodiments, one or more of the following genes may be analyzed to determine a type and / or severity of aninflammatory bowel disorder: 'SLC6A4', 'C8orf58', 'ZCWPW1', 'NR2F1-AS1', 'LINC00482', 'AURKC, 'CCDC120', 'FENDRR', 'KIF9', and / or 'TESMIN'. In some embodiments, one or more of the following genes may be analyzed to determine a type and / or severity of an inflammatory bowel disorder: 'WDR26', 'TMEM88B', 'NR2F1', 'PLXNB2', 'PXDN', 'FAM155A', 'KCNQ2', 'BAIAP2L1', 'CST3', and / or 'SYCE3'. In some embodiments, one or more of the following genes may be analyzed to determine a type and / or severity of an inflammatory bowel disorder: 'ECHS1', 'UNC80', 'PNKD', 'CRYBB2', 'KIF25-AS1', 'APOH', 'TSPYL2', 'CELF4', 'HAR1B', and / or 'SNORA23'. In some embodiments, one or more of the genes disclosed herein may be fed into a classifier to determine a type and / or severity of an inflammatory bowel disorder. In some embodiments, relative enrichment or relative depletion of 'C3' may be analyzed to determine a type and / or a severity of an inflammatory bowel disorder. In some embodiments, relative enrichment or relative depletion of 'SNURF' may be analyzed to determine a type and / or a severity of an inflammatory bowel disorder. In some embodiments, relative enrichment or relative depletion of ‘NR2FE may be analyzed to determine a type and / or a severity of an inflammatory bowel disorder. In some embodiments, relative enrichment or relative depletion of ‘GPUFBPl’ may be analyzed to determine a type and / or a severity of an inflammatory bowel disorder. In some embodiments, relative enrichment or relative depletion of ‘HTT’ may be analyzed to determine a type and / or a severity of an inflammatory bowel disorder. In some embodiments, relative enrichment or relative depletion of ‘SNORA23' may be analyzed to determine a type and / or a severity of an inflammatory bowel disorder.

[0148] In some embodiments, one or more genes may be relatively enriched or relatively depleted in a patient sample for a patient who has a disease as compared to a healthy control sample. In some embodiments, one or more genes may be relatively enriched or relatively depleted in a patient sample for a patient who has a disease as compared to a sample from a patient in remission. In some embodiments, one or more genes may be relatively enriched or relatively depleted in a patient sample for a patient who has a disease in remission as compared to a healthy control sample. In some embodiments, one or more genes may be relatively enriched or relatively depleted in a patient sample for a patient who has Crohn’s disease as compared to a healthy control sample. In some embodiments, one or more genes may be relatively enriched or relatively depleted in a patient sample for a patient who has ulcerative colitis as compared to a healthy control sample. In some embodiments, one or more genes may be relatively enriched or relatively depleted in a patient sample for a patient who has Crohn’s disease as compared to a sample from a patient who has ulcerative colitis. In some embodiments, one or more genes may be relatively enriched or relatively depleted in a patient sample for a patient who has a severe disease as compared to ahealthy control sample. In some embodiments, one or more genes may be relatively enriched or relatively depleted in a patient sample for a patient who has a moderate disease as compared to a healthy control sample. In some embodiments, one or more genes may be relatively enriched or relatively depleted in a patient sample for a patient who has a mild disease as compared to a healthy control sample. In some embodiments, one or more genes may be relatively enriched or relatively depleted in a patient sample for a patient who has a severe disease as compared to a sample from a patient who has a moderate disease. In some embodiments, one or more genes may be relatively enriched or relatively depleted in a patient sample for a patient who has a severe disease as compared to a sample from a patient who has a mild disease. In some embodiments, one or more relatively enriched or relatively depleted genes may be fed into a classifier or a trained algorithm. In some embodiments, a relatively enriched or relatively depleted gene may meet a statistical significance of p <0.05 or <0.01. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has Crohn’s disease compared to a healthy control sample: 'NR0B1', 'NDP', 'ZBTB8B', 'PRICKLE3', 'SYP- AS1', 'TSPYL2', 'ZMYM3', 'NEXMIF', 'MAGEE2', 'BRWD3', 'TAF7L', 'GUCY2F', 'SIX3', 'RHOXF1P1', 'RHOXF1', 'FAM122B', 'MMGTF, 'L1CAM', 'HCFC1', 'LINC01119', 'ANKRD36BP2', 'C1QTNF12', 'COLECI 1', 'ASTL', 'LINC01918', 'ERICH6', 'PYDC2', 'IQUB', 'SNAPC4', 'EDF1', 'IL36RN', 'WASH2P', 'OR7G3', 'PTPN4', 'LINC01756', 'HMGB4', 'MYO7B', 'FAM168A', 'UBE2L5', 'SCAT1', 'THSD7B', 'LOC100505585', 'PLEKHA4', 'DCDC2C, 'BMS1P14', 'ORC4', 'ANO7', 'MBD5', 'HLA-F', 'FAM71F1', 'FLJ43315', 'OBP2A', 'GTPBP6', 'PRRG3', 'LBX1', 'ECHS1', 'GPRIN2', 'GLUD1', 'FBXO3', 'MMP26', 'OCLM', 'TYR', 'NFASC, 'SNAP47', 'PROZ', 'KCNAB2', 'SMG1', 'GPR139', 'SCNN1B', 'RFWD3', 'CSH2', 'IGFL2', 'GNG8', 'CCDC155', 'C19orf81', 'HSPA12B', 'STMN3', 'LOC401021', 'RNA5-8SN5', 'RNA28SN5', 'IRS1', 'SH3BP1', 'RAB1A', 'NEUROD1', 'DNAJB8-AS1', 'TM4SF1', 'TM4SF1- AS1', 'FLJ42393', 'ZNF662', 'C3orfl8', 'FAM153CP', 'NIM1K', 'ERAP1', 'LAMA4', 'RPS6KA2', 'BICRAL', 'SVOPL', 'NM 001371249', 'AGR3', 'GLI3', 'MMD2', 'BHLHA15', 'DDX11L5', 'PRDM12', 'FUT7', 'SHOX', 'GCNA', 'PABPC5', 'UNC80', 'PNKD', 'SP140', 'F AMI IOC, 'ALKAL2', 'PXDN', 'SF3B6', 'EIF2AK2', 'SIX3-AS1', 'NRXN1', 'LOC730100', 'LRRC42', 'MEGF6', 'IL1B', 'CACNB4', 'RBMS1', 'LRP2', 'DLX1', 'SP3', 'RFTN2', 'IKZF2', 'NM_001371275', 'NM_001371276', 'NM_001371277', 'NM_001371274', 'AP1S3', 'SP110', 'NGEF', 'SLC6A1', 'UBE2E2', 'ITGA9-AS1', 'CTDSPL', 'KLHL18', 'SEMA3F', 'HES3', 'ADGRL2', 'BBX', 'CD200', 'GSK3B', 'STXBP5L', 'FAIM', 'ERICH6-AS1', 'LRRC77P', 'FNDC3B', 'CHRD', 'LOC107986163', 'SEC13', 'CCK', 'KIF9', 'SHISA5', 'SEMA3F-AS1', 'CCDC66', 'PER3', 'LSAMP', 'ZNF148', 'UROC1', 'NPHP3', 'NPHP3-ACAD11', 'CLRN1','SHOX2', 'SLITRK3', 'GMNC', 'RAP1A', 'LOC105374338', 'PCGF3', 'HTT', 'LINC00955', 'MSX1', 'PCDH7', 'DCUN1D4', 'SYCP1', 'ADGRL3', 'UGT8', 'CPLX1', 'RNF212', 'NELFA', 'TNIP2', 'LDB2', 'CCKAR', 'TLR6', 'GABRA2', 'UTP3', 'HPSE', 'CXXC4', 'ALPK1', 'QRFPR', 'NPR1', 'ZNF827', 'MAB21L2', 'DCHS2', ENPP6', 'IRF2', 'ZBTB7B', 'SLC6A19', 'SPEF2', 'SV2C, 'F2R', 'MEF2C-AS2', 'MEF2C-AS1', 'NR2F1', 'CARMN', 'FOXIl', 'CPLX2', EIF4E1B', 'TPPP', 'SLC12A7', 'RETREG1', 'BASP1-AS1', 'NUP155', 'NR2F1-AS1', 'MCTP1', 'CCDC112', 'ZCCHC10', 'PBX1', 'MIR4281', 'PRRX1', E2F3', 'BTN2A2', 'AIFl', 'MIR219A1', 'SYNGAP1', 'BRPF3', 'RAB44', 'LINC02520', 'TTLL10', 'FOXO3', 'MYB', EXOC2', 'MIR4645', 'GABBR1', 'RGL2', 'CUT A', 'CPNE5', 'MIR4462', 'MDGA1', 'TBCC, 'PKHD1', EYS', 'HDDC2', 'NCOA7- ASl', 'HIVEP2', 'MIR4466', 'LINC00473', 'KIF25-AS1', 'FOXK1', 'SLC29A4', 'SHISA4', 'VSTM2A', 'NIPSNAP2', 'CCT6P3', 'ZP3', 'MYH16', 'LOC105375423', 'MUC17', 'SERPINEF, 'COL26A1', 'CDK18', 'PRKAR2B', 'LRRN3', 'LRGUK', EN2', 'PDGFA', 'HRAT92', 'CARD11', 'IGF2BP3', ERVW-1', 'BAIAP2L1', 'LAMTOR4', 'ZCWPW1', 'C7orf61', 'TSC22D4', 'MOGAT3', 'CNPY1', 'KBTBDH', 'LOC100287015', 'MCPH1', 'C8orf74', 'C8orf58', 'RBPMS', 'SDC2', 'LOC105375690', 'LOC 101927822', 'JRK', 'C8orfH', 'GPUffiPl', 'LOC 101928902', 'ADCK5', ERICH1', 'MIR124-1', 'GFRA2', 'ACTN2', 'ZFHX4', 'ZFHX4-AS1', 'SNX16', 'TP53INP1', 'BAALC-AS1', 'KLHL38', 'LRRC6', 'TG, 'TRAPPC9', 'PTK2', 'SLURPF, 'SCRT1', 'CDKN2B- AS1', 'TMEM8B', 'Clorfl59', 'CROCC, 'ZNF462', 'TMEM240', 'LHX2', 'STXBP1', 'FAAP20', 'SURF2', 'BRD3OS', 'LCN9', 'MIR4674', 'NALT1', 'ARRDC1', and / or 'PTPRD-AS1'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has Crohn’s disease compared to a healthy control sample: 'C3', 'SNURF', 'SNRPN', 'NM_001371415', 'ACE2', 'TMEM259', 'FANCF', 'C21orf62-ASl', 'STXBP1', 'ZCCHC10', 'ZNF148', 'GPUffiPl', 'PAXBP1', 'AIFl', 'POFUT2', 'SCAT1', 'LINC00205', 'MMGT1', 'SIGLEC15', 'SNAPC4', 'LINC01970', 'SLC6A4', 'C8orf58', 'ZCWPW1', 'NR2F1-AS1','LINCOO482', 'AURKC, 'CCDC120', 'FENDRR', 'KIF9', 'TESMIN', 'WDR26', 'TMEM88B', 'NR2F1', 'PLXNB2', 'PXDN', 'FAM155A', 'KCNQ2', 'BAIAP2L1', 'CST3', 'SYCE3', ECHS1', 'UNC80', 'PNKD', 'CRYBB2', 'KIF25-AS1', 'APOH', 'TSPYL2', 'CELF4', and / or 'HAR1B'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has ulcerative colitis compared to a healthy control sample: 'LOC 101928626', 'TMEM88B', 'CDKN2A', ELAVL2', 'FAM205BP', 'DNAJB5-DT', 'FAM221B', 'LINC01410', 'NXNL2', 'NM_001371194', 'HDHD3', 'BRINP1', 'RC3H2', 'SCAI', 'FIBCDl', 'SURF1', 'NOTCH1', 'LCN8', 'PNPLA7', 'LINC00707', 'OPTN', 'MSRB2', 'NRBF2', 'COL13A1', 'CHST3', 'MARVELD1', 'ADRB1', 'GPR26', 'CAMK2N1', 'LINC00706', TTIH5', 'GATA3-AS1', 'UPF2', 'LOC105376453', 'C10orf67', 'PRTFDC1','ARHGAP22', 'ASAP3', 'ADAMTS14', 'BLNK', 'LBX1-AS1', 'CALHM2', 'EMX2', 'EMX20S', 'RGS10', 'ClOorfPl', 'SYCE1', 'FAM99B', 'KCNQ1', 'MRGPRG-AS1', 'AKIP1', 'SNORA23', 'SAA1', 'FBXO3-DT', 'FAM111A', 'MS4A12', 'MS4A10', 'NAA40', 'SPDYC, 'SLC22A20P', 'SNX32', 'CTTN', 'CBL', 'MRPS15', 'PKNOX2', 'INS', 'CD81-AS1', 'DCHS1', 'ST5', 'FANCF', 'ALX4', 'PHF21A', 'YPEL4', 'SLC15A3', 'SLC22A6', 'TBX10', 'TESMIN', 'GPR83', 'SLC35F2', 'EXPH5', 'OPCML', 'RAB3B', 'ATN1', 'AEBP2', 'PLPP3', 'HOXC8', 'ZNF385A', 'MSRB3', 'RNFT2', 'PIWILr, 'ULK1', 'P2RX2', 'LM03', 'LOC100288798', 'PCED1B', 'AMIG02', 'ZNF641', 'MAP3K12', 'TMEM119', 'C12orf49', 'KSR2', 'RIMBP2', 'SPATA13', 'SOX1', 'F7', 'GJB2', 'LINC00539', 'LINC01058', 'LHFPL6', 'RUBCNL', 'PCDH20', 'POU4F1', 'FAM155A', 'LINC00567', 'LOC107985184', 'ARHGAP5', 'PLEKHG3', 'TBX15', 'SERPINA3', 'BDKRB1', 'PPP2R5C, 'HOMEZ', 'ZFHX2', 'JPH4', 'SFTA3', 'NKX2-1-AS1', 'MDGA2', 'BMP4', 'KCNH5', 'TTC7B', 'TEDC1', 'SNRPN', 'SNURF', 'LINC02352', 'LOC101928134', 'RYR3', 'SLC24A5', 'GCNT3', 'GBA', 'CASC4', 'NEDD4', 'MEGF11', 'SNUPN', 'ISL2', 'CTSH', 'Clorf61', 'LINC02351', 'PDIA2', 'WFIKKN1', 'UBE2I', 'CACNG3', 'SELENON', 'MT4', 'ADGRG1', 'MARVELD3', 'OSGIN1', 'CDT1', 'DPEP1', 'SPIRE2', 'RGS11', 'MRPL28', 'TPSB2', 'HS3ST6', 'PRSS33', 'DEDD', 'LINC01570', 'SNX29', 'XYLT1', 'TLCD3B', 'FBXL19-AS1', 'IRX5', 'NLRC5', 'DERPC, 'COTL1', 'FENDRR', 'SELL', 'MIR199A2', 'DNM3OS', 'MTRNR2L1', 'TNR', 'SUZ12P1', 'ASTN1', 'MLLT6', 'CNTNAP1', 'CRHR1', 'SGCA', 'LOC100507002', 'RGS9', 'SLC26A11', 'TBCD', 'RTN4RL1', 'MIR132', 'MIR212', 'P2RX1', 'PHF23', 'DHRS13', 'SLC6A4', 'CCL16', 'KRT10', 'CACNA1S', 'HOXB13', 'MRC2', 'APOH', 'CACNG4', 'AATK', 'LINC00482', ’CSNK1D’, ’LINC01970', 'DLGAP1-AS5', 'TWSG1', 'RAB31', 'APCDD1', 'ANKRD62', 'SIGLEC15', 'GRP', 'CELF4', 'MADCAM1', 'HCN2', 'CELF5', 'NFIC, 'FSD1', 'ALKBH7', 'VAV1', 'ARHGEF18', 'ANGPTL4', 'C19orf38', 'DCAF15', 'LINC00661', 'PROX1-AS1', 'PROXI', 'CRTC1', 'TDRD12', 'FXYD1', 'FXYD5', 'CATSPERG', 'IFNL1', 'MIA3', 'MIR8085', 'HIF3A', 'ZNF114', 'WDR26', 'FLT3LG', 'MIRLET7E, 'SPACA6', 'BRSK1', 'TMEM190', 'ZNF444', 'ZNF71', 'AURKC, 'CENPBD1P1', 'R3HDM4', 'TMEM259', 'JMJD4', 'MRPL55', 'OBSCN-AS1', 'HIST3H3', 'TICAM1', 'CD70', 'C3', 'CD209', 'CTXN1', 'ADAMTS10', 'ZNF558', 'ZNF846', 'KANK2', 'EPOR', 'H00K2', 'PODNL1', 'ASF IB', 'FAM89A', 'HAPLN4', 'PCNX2', 'TSHZ3', 'ATP4A', 'LINC01529', 'LINC01132', 'CYP2A6', 'PVR', 'DM1-AS', 'SIX5', 'SLC8A2', 'CAir, 'LRRC4B', 'KLK14', 'MIR4428', 'HAS1', 'ZNF350', 'ZNF677', 'CDC42EP5', 'RDH13', 'SHISA7', 'SBK3', 'RAD21L1', 'DSTN', 'KCNK15', 'LOC105372633', 'ARFGEF2', 'TSHZ2', 'DOK5', 'ADRM1', 'COL20A1', 'MHENCR', 'OPRL1', 'CENPB', 'TMX4', 'CST3', 'AHCY', 'TGM2', 'OSER1', 'OSER1-DT', 'EPPIN', 'EPPIN-WFDC6', 'ELMO2', 'KCNB1', 'PTGIS', 'APCDD1L', 'APCDD1L-DT', 'LINC00659', 'HAR1B', 'KCNQ2', 'SRMS', 'ZNF512B', 'OLIG1','LOC105369306', 'ETS2', 'LINC02575', 'LINC00205', 'BAGE', 'PAXBP1', 'C21orf62-ASl', 'ERG', 'DSCAM', 'DNMT3L', 'UBE2G2', 'P0FUT2', 'DIP2A', 'CRYBB2', 'MY018B', 'LOC91370', 'GAREM2', 'ATXN10', 'KLHL22', 'GRK3', 'LINC01460', 'LOC105374378', 'SSTR3', 'BAIAP2L2', 'POLR3H', 'MIR378I', 'NM 001371417', 'PLXNB2', 'PPP6R2', 'SYCE3', 'PLCXD1', 'CSF2RA', 'CD99P1', 'TIMP1', 'CCDC120', 'NONO', 'CHIC1', 'SLC16A2', 'DRP2', 'LCK', 'NRK', 'LOC101928358', 'TMEM164', 'XPNPEP2', 'MBNL3', 'FAM122C, 'MAMLD1', 'MAGEA1', 'TMEM187', 'MIR6089', 'PRKX', 'NM_001371415', 'ACE2', 'NR0B1', 'NDP', 'ZBTB8B', 'PRICKLE3', 'SYP-AS1', 'TSPYL2', 'ZMYM3', 'NEXMIF', 'MAGEE2', 'BRWD3', 'TAF7L', 'GUCY2F', 'SIX3', 'RHOXF1P1', 'RHOXF1', 'FAM122B', 'MMGT1', 'L1CAM', 'HCFC1', 'LINC01119', 'ANKRD36BP2', 'C1QTNF12', 'COLECI 1', 'ASTL', 'LINC01918', 'ERICH6', 'PYDC2', 'IQUB', 'SNAPC4', 'EDF1', 'IL36RN', 'WASH2P', 'OR7G3', 'PTPN4', 'LINC01756', 'HMGB4', 'MYO7B', 'FAM168A', 'UBE2L5', 'SCAT1', 'THSD7B','LOC100505585', 'PLEKHA4', 'DCDC2C, 'BMS1P14', 'ORC4', 'ANO7', 'MBD5', 'HLA-F', 'FAM71F1', 'FLJ43315', 'OBP2A', 'GTPBP6', 'PRRG3', 'LBX1', 'ECHS1', 'GPRIN2', 'GLUD1', 'FBXO3', 'MMP26', 'OCLM', 'TYR', 'NFASC, 'SNAP47', 'PROZ', 'KCNAB2', 'SMG1', 'GPR139', 'SCNN1B', 'RFWD3', 'CSH2', 'IGFL2', 'GNG8', 'CCDC155', 'C19orf81', 'HSPA12B', 'STMN3', 'LOC401021', 'RNA5-8SN5', 'RNA28SN5', 'IRS1', 'SH3BP1', 'RAB1A', 'NEUROD1', 'DNAJB8- AS1', 'TM4SF1', 'TM4SF1-AS1', 'FLJ42393', 'ZNF662', 'C3orfl8', 'FAM153CP', 'NIM1K', 'ERAP1', 'LAMA4', 'RPS6KA2', 'BICRAL', 'SVOPL', 'NM OO 1371249', 'AGR3', 'GLI3', 'MMD2', 'BHLHA15', 'DDX11L5', 'PRDM12', 'FUT7', 'NR 137295', 'SHOX', 'GCNA', 'PABPC5', 'UNC80', 'PNKD', 'SP140', 'F AMI IOC, 'ALKAL2', 'PXDN', 'SF3B6', 'EIF2AK2', 'SIX3-AS1', 'NRXN1', 'LOC730100', 'LRRC42', 'MEGF6', 'IL1B', 'CACNB4', 'RBMS1', 'LRP2', 'DLX1', 'SP3', 'RFTN2', 'IKZF2', 'NM_001371275', 'NM_001371276', 'NM_001371277', 'NM_001371274', 'AP1S3', 'SP110', 'NGEF', 'SLC6A1', 'UBE2E2', 'ITGA9-AS1', 'CTDSPL', 'KLHL18', 'SEMA3F', 'HES3', 'ADGRL2', 'BBX', 'CD200', 'GSK3B', 'STXBP5L', 'FAIM', 'ERICH6-AS1', 'LRRC77P', 'FNDC3B', 'CHRD', 'LOC107986163', 'SEC13', 'CCK', 'KIF9', 'SHISA5', 'SEMA3F-AS1', 'CCDC66', 'PER3', 'LSAMP', 'ZNF148', 'UROC1', 'NPHP3', 'NPHP3-ACAD11', 'CLRN1', 'SHOX2', 'SLITRK3', 'GMNC', 'RAP1A', 'LOC105374338', 'PCGF3', 'HTT', 'LINC00955', 'MSX1', 'PCDH7', 'DCUN1D4', 'SYCP1', 'ADGRL3', 'UGT8', 'CPLX1', 'RNF212', 'NELFA', 'TNIP2', 'LDB2', 'CCKAR', 'TLR6', 'GABRA2', 'UTP3', 'HPSE, 'CXXC4', 'ALPK1', 'QRFPR', 'NPR1', 'ZNF827', 'MAB21L2', 'DCHS2', 'ENPP6', 'IRF2', 'ZBTB7B', 'SLC6A19', 'SPEF2', 'SV2C, 'F2R', 'MEF2C-AS2', 'MEF2C-AS1', 'NR2F1', 'CARMN', 'FOXI1', 'CPLX2', 'EIF4E1B', 'TPPP', 'SLC12A7', 'RETREG1', 'BASP1-AS1', 'NUP155', 'NR2F1-AS1', 'MCTP1', 'CCDC112', 'ZCCHC10', 'PBX1', 'MZR4281', 'PRRX1', 'E2F3', 'BTN2A2', 'AIF1', 'MIR219A1', 'SYNGAP1','BRPF3', 'RAB44', 'LINC02520', 'TTLL10', 'FOXO3', 'MYB', 'EXOC2', 'MIR4645', 'GABBR1', 'RGL2', 'CUT A', 'CPNE5', 'MIR4462', 'MDGA1', 'TBCC, 'PKHD1', 'EYS', 'HDDC2', 'NCOA7- ASl', 'HIVEP2', 'MIR4466', 'LINC00473', 'KIF25-AS1', 'FOXK1', 'SLC29A4', 'SHISA4', 'VSTM2A', 'NIPSNAP2', 'CCT6P3', 'ZP3', 'MYH16', 'LOC105375423', 'MUC17', 'SERPINEF, 'COL26A1', 'CDK18', 'PRKAR2B', 'LRRN3', 'LRGUK', 'EN2', 'PDGFA', 'HRAT92', 'CARD11', 'IGF2BP3', 'ERVW-1', 'BAIAP2L1', 'LAMTOR4', 'ZCWPW1', 'C7orf61', 'TSC22D4', 'MOGAT3', 'CNPY1', 'KBTBDH', 'LOC100287015', 'MCPH1', 'C8orf74', 'C8orf58', 'RBPMS', 'SDC2', 'LOC105375690', 'LOC 101927822', 'JRK', 'C8orfH', 'GPIHBP1', 'LOC 101928902', 'ADCK5', 'ERICH1', 'MIR124-1', 'GFRA2', 'ACTN2', 'ZFHX4', 'ZFHX4-AS1', 'SNX16', 'TP53INP1', 'BAALC-AS1', 'KLHL38', 'LRRC6', 'TG', 'TRAPPC9', 'PTK2', 'SLURPF, 'SCRT1', 'CDKN2B- AS1', 'TMEM8B', 'Clorfl59', 'CROCC, 'ZNF462', 'TMEM240', 'LHX2', 'STXBP1', 'FAAP20', 'SURF2', 'BRD3OS', 'LCN9', 'MIR4674', 'NALT1', 'ARRDC1', 'PTPRD-AS1'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has ulcerative colitis compared to a healthy control sample: 'ACE2', 'C3', 'NM_001371415', 'SNURF', 'TMEM259', 'SNRPN', 'FANCF', 'ZNF148', 'ZCCHC10', 'C21orf62-ASl', 'SCAT1', 'LINC00482', 'PAXBP 1', 'STXBP1', 'MMGT1', 'NR2F1- AS1', 'NR2F1', 'SYCE3', 'KIF9', 'SNAPC4', 'FENDRR', 'AIF1', 'POFUT2', 'APOH', 'LINC01970', 'SIGLEC15', 'AURKC, 'PNKD', 'SLC6A4', 'LINC00205', 'PXDN', 'HTT', 'AGR3', 'ZCWPW1', 'MYH16', 'FAM155A', 'KIF25-AS1', 'CRYBB2', 'HAR1B', 'C8orf58', 'WDR26', 'DRP2', 'GPR139', 'CYP2A6', 'SGCA', 'OPTN', 'CST3', 'SBK3', 'PLXNB2', and / or 'ISL2'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has ulcerative colitis as compared to a sample from a patient who has Crohn’s disease: 'LOC 101928626', 'TMEM88B', 'CDKN2A', 'FAM205BP', 'FAM221B', 'NXNL2', 'NM 001371194', 'HDHD3', 'RC3H2', 'SCAI', 'FIBCDl', 'SURF1', 'NOTCH1', 'LCN8', 'PNPLA7', 'MSRB2', 'NRBF2', 'COL13A1', 'CHST3', 'MARVELD1', 'ADRB1', 'GPR26', 'CAMK2N1', TTIH5', 'UPF2', 'LOC105376453', 'ASAP3', 'LBX1-AS1', 'CALHM2', 'EMX2', 'EMX2OS', 'RGS10', 'C10orf91', 'SYCE1', 'FAM99B', 'KCNQ1', 'AKIPl', 'SNORA23', 'FBXO3- DT', 'FAM111A', 'MS4A10', 'NAA40', 'SLC22A20P', 'SNX32', 'CTTN', 'CBL', 'MRPS15', 'PKNOX2', 'CD81-AS1', 'DCHS1', 'ST5', 'FANCF', 'YPEL4', 'SLC15A3', 'TBX10', 'TESMIN', 'EXPH5', 'OPCML', 'RAB3B', 'AEBP2', 'HOXC8', 'ZNF385A', 'MSRB3', 'PIWILr, 'ULK1', 'P2RX2', 'LOC100288798', 'ZNF641', 'MAP3K12', 'C12orf49', 'RIMBP2', 'SOX1', 'F7', 'GJB2', 'LINC01058', 'POU4F1', 'LINC00567', 'LOC107985184', 'PLEKHG3', 'HOMEZ', 'ZFHX2', 'JPH4', 'SFTA3', 'NKX2-1-AS1', 'MDGA2', 'BMP4', 'TTC7B', 'TEDC1', 'SNRPN', 'SNURF', 'LINC02352', 'LOC101928134', 'GCNT3', 'GBA', 'CASC4', 'NEDD4', 'MEGF11', 'SNUPN','ISL2', 'CTSH', 'Clorf61', 'LINC02351', 'PDIA2', 'WFIKKN1', 'SELENON', 'ADGRG1', 'MARVELD3', 'OSGIN1', 'CDT1', 'DPEP1', 'SPIRE2', 'RGS11', 'MRPL28', 'TPSB2', 'HS3ST6', 'PRSS33', 'DEDD', 'LINC01570', 'SNX29', 'TLCD3B', 'NLRC5', 'DERPC, 'COTL1', 'FENDRR', 'MTRNR2LF, 'SUZ12P1', 'MLLT6', 'CNTNAP1', 'CRHR1', 'SGCA', 'LOC100507002', 'RGS9', 'SLC26A11', 'TBCD', 'RTN4RL1', 'MIR132', 'MIR212', 'P2RX1', 'PHF23', 'SLC6A4', 'CCL16', 'KRT10', 'MRC2', 'AATK', 'CSNK1D', 'TWSG1', 'RAB31', 'APCDD1', 'ANKRD62', 'SIGLEC15', 'MADCAM1', 'HCN2', 'CELF5', 'NFIC, 'FSD1', 'ALKBH7', 'VAV1', 'ANGPTL4', 'C19orf38', 'DCAF15', 'LINC00661', 'PROX1', 'CRTC1', 'TDRD12', 'FXYD1', 'FXYD5', 'CATSPERG', 'MIA3', 'MIR8085', 'HIF3A', 'WDR26', 'FLT3LG', 'MIRLET7E', 'SPACA6', 'BRSK1', 'TMEM190', 'ZNF444', 'ZNF71', 'AURKC, 'R3HDM4', 'TMEM259', 'JMJD4', 'MRPL55', 'OBSCN-AS1', 'HIST3H3', 'TICAM1', 'C3', 'CD209', 'CTXN1', 'ADAMTS10', 'ZNF558', 'ZNF846', 'KANK2', 'HOOK2', 'PODNL1', 'ASF1B', 'FAM89A', 'HAPLN4', 'PCNX2', 'TSHZ3', 'ATP4A', 'LINC01529', 'LINC01132', 'PVR', 'DM1-AS', 'SLC8A2', 'CA11', 'MIR4428', 'HAST, 'ZNF350', 'ZNF677', 'CDC42EP5', 'SHISA7', 'SBK3', 'RAD21L1', 'DSTN', 'LOC105372633', 'ARFGEF2', 'DOK5', 'ADRM1', 'COL20A1', 'MHENCR', 'OPRL1', 'CENPB', 'CST3', 'TGM2', 'OSER1', 'OSER1-DT', 'ELMO2', 'KCNB1', 'PTGIS', 'LINC00659', 'ZNF512B', 'LOC105369306', 'ETS2', 'LINC02575', 'LINC00205', 'ERG', 'DNMT3L', 'UBE2G2', 'POFUT2', 'DIP2A', 'GAREM2', 'ATXN10', 'KLHL22', 'GRK3', 'LINC01460', 'LOC105374378', 'POLR3H', 'MIR378I', 'NM 001371417', 'SYCE3', 'PLCXD1', 'CSF2RA', 'TIMPl', 'CCDC120', 'CHIC1', 'SLC16A2', 'NRK', 'LOC101928358', 'TMEM164', 'XPNPEP2', 'MBNL3', 'FAM122C, 'MAMLD1', 'MAGEA1', 'TMEM187', 'NM 001371415', 'ACE2', 'NDP', 'PRICKLE3', 'SYP-AS1', 'TSPYL2', 'NEXMIF', 'MAGEE2', 'TAF7L', 'GUCY2F', 'SIX3', 'RHOXF1P1', 'RHOXF1', 'FAM122B', 'L1CAM', 'HCFC1', 'LINC01119', 'ANKRD36BP2', 'COLECI 1', 'ASTL', 'LINC01918', 'ERICH6', 'IQUB', 'SNAPC4', 'EDF1', 'PTPN4', 'HMGB4', 'UBE2L5', 'THSD7B', 'LOC100505585', 'PLEKHA4', 'DCDC2C, 'BMS1P14', 'ORC4', 'ANO7', 'MBD5', 'HLA-F', 'FLJ43315', 'OBP2A', 'GTPBP6', 'LBX1', 'ECHS1', 'GPRIN2', 'FBXO3', 'NFASC, 'SNAP47', 'PROZ', 'KCNAB2', 'SMG1', 'RFWD3', 'CSH2', 'GNG8', 'CCDC155', 'C19orf81', 'HSPA12B', 'SH3BP1', 'NEUROD1', 'DNAJB8-AS1', 'FLJ42393', 'C3orfl8', 'FAM153CP', 'NIM1K', 'ERAP1', 'RPS6KA2', 'BICRAL', 'NM OO 1371249', 'GLI3', 'MMD2', 'BHLHA15', 'DDX11L5', 'PRDM12', 'FUT7', 'NR 137295', 'GCNA', 'UNC80', 'PNKD', 'F AMI IOC, 'ALKAL2', 'SF3B6', 'EIF2AK2', 'NRXN1', 'LOC730100', 'LRRC42', 'MEGF6', 'CACNB4', 'SP3', 'RFTN2', KZF2', 'NM_001371275', 'NM_001371276', 'NM_001371277', 'NM_001371274', 'AP1S3', 'NGEF', 'SLC6A1', 'UBE2E2', TTGA9-AS1', 'CTDSPL', 'KLHL18', 'SEMA3F', 'HES3', 'GSK3B', 'ERICH6-AS1', 'FNDC3B', 'CHRD', 'LOC107986163', 'KIF9', 'SHISA5', 'SEMA3F-AS1','CCDC66', 'PER3', 'LSAMP', 'ZNF148', 'UR0C1', 'NPHP3', 'NPHP3-ACAD11', 'CLRN1', 'SHOX2', 'RAP1A', 'LOC105374338', 'PCGF3', HTT', 'LINC00955', 'PCDH7', 'DCUN1D4', 'UGT8', 'CPLX1', 'RNF212', 'NELFA', 'TNTP2', 'CCKAR', 'GABRA2', 'UTP3', 'HPSE, 'ALPK1', 'NPR1', 'ZNF827', 'DCHS2', 'ZBTB7B', 'MEF2C-AS1', 'EIF4E1B', 'TPPP', 'SLC12A7', 'RETREG1', 'NUP155', 'MCTP1', 'CCDC112', 'ZCCHC10', 'PBX1', 'MIR4281', 'PRRX1', 'E2F3', 'AIF1', 'SYNGAP1', 'BRPF3', 'TTLL10', 'FOXO3', 'MYB', 'EXOC2', 'GABBR1', 'RGL2', 'CUTA', 'CPNE5', 'MIR4462', 'TBCC, 'PKHD1', HDDC2', 'NCOA7-AS1', HIVEP2', 'MIR4466', 'KIF25- ASl', 'SLC29A4', 'SHISA4', 'CCT6P3', 'LOC105375423', 'MUC17', 'COL26A1', 'PRKAR2B', 'LRRN3', 'EN2', 'PDGFA', HRAT92', 'IGF2BP3', 'BAIAP2L1', 'LAMTOR4', 'C7orf61', 'TSC22D4', 'MOGAT3', 'LOC100287015', 'MCPH1', 'C8orf74', 'RBPMS', 'SDC2', 'LOC105375690', 'JRK', 'GPHTBPl', 'LOC101928902', 'ADCK5', 'ERICH1', 'MIR124-1', 'GFRA2', 'TP53INP1', 'KLHL38', 'LRRC6', 'TRAPPC9', 'PTK2', 'SLURP1', 'CDKN2B-AS1', 'TMEM8B', 'CROCC, 'TMEM240', 'LHX2', 'STXBP1', 'FAAP20', 'SURF2', 'BRD3OS', 'LCN9', 'MIR4674', 'NALT1', 'ARRDC1', and / or 'PTPRD-AS1'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has ulcerative colitis as compared to a sample from a patient who has Crohn’s disease: 'SNORA23', 'AIF1', 'HTT', 'FANCF', 'ASF1B', 'TMEM259', 'ERG', 'LOC105372633', 'SNURF', 'C3', 'SNRPN', 'TMEM164', 'PLEKHG3', 'LAMTOR4', 'FAM221B', 'PDGFA', 'HRAT92', 'ELMO2', 'JPH4', 'NM_001371249', 'LOC105374338', 'MS4A10', 'CHIC1', 'BMS1P14', 'KANK2', 'TICAM1', 'TNIP2', 'CROCC, 'EDF1', 'NM 001371415', HOMEZ', 'PLCXD1', 'SNUPN', 'WFIKKNl', 'TDRD12', 'HAST, 'ECHS1', 'EXOC2', 'PTK2', 'LCN8', 'ASAP3', 'C19orf38', 'UROC1', 'LINC02575', 'TBCC, 'CDKN2A', 'BRD3OS', 'CDKN2B-AS1', 'DCUN1D4', and / or 'CCDC120'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has mild ulcerative colitis as compared to a sample from a patient who has moderate ulcerative colitis: 'RHO', 'CASC4', 'KLK9', 'HSPA12B', 'NM 001371415', 'LIF', 'RTN4RL1', 'MAML3', 'HCN2', 'FLCN', 'MIA3', 'LINC01410', 'CRYBB2', 'LOCI 12268114', 'CHST3', 'MBNL3', 'C3', 'PUS1', 'ACE2', 'LTBP3', and / or 'OLIG2'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has mild ulcerative colitis as compared to a sample from a patient who is in remission from ulcerative colitis: 'MIA3', 'RHO', HCN2', 'OLIG2', 'MAML3', 'SDC2', 'TBX10', 'FBXO3', 'MAGEF1', 'RUBCNL', 'KANK2', 'ARHGEF18', 'ACE2', 'NUP155', 'ULK1', 'SUOX', 'LRMDA', 'CRYBB2', 'FBXO3-DT', 'RAB44', 'AHCY', 'LTBP3', 'MIR7-3HG', 'MIR212', 'ASGR2', 'PUS1', 'TMEM259', 'PAPPA', HSPA12B', 'ANKRD36BP2', 'CCDC120', 'EIF2AK2', 'MBNL3', 'RSPH6A', 'EDNRB', 'LOC100287015','PTGIS', 'GMNC', 'DNAJB8-AS1', 'SIX5', 'MCPH1', 'TBX15', 'MIR451B', 'RPS6KA2', 'ASH1L', 'LINC00955', 'STC2', 'SGCA', 'VWF', and / or 'LOC91370'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has mild ulcerative colitis as compared to a sample from a patient who has severe ulcerative colitis: 'GDPD5', 'FBXO27', 'F AMI IOC, 'NM_001371343', 'GFI1B', 'IFI27L2', 'KLHL22', 'CARMILl', 'N0VA1', 'EXOC2', 'CDKN2A', 'HPSE', 'COLECI 1', HIVEP2', 'OSER1', 'SNCB', 'C6orfl32', 'ANGPTL4', 'CDKN2B-AS1', 'LOC105376453', 'C19orf81', 'GPR182', 'CHMP1A', 'SURF2', HCK', 'CNTNAP1', 'JRK', 'DNAJB8-AS1', 'NCOA7-AS1', 'ADRB1', 'FAAP20', 'EIF4E1B', 'SEL1L3', H0XC8', 'CTTN', 'FBXW4', 'R3HDM4', 'BAIAP2L1', 'LINC01970', 'ZNF677', 'SBK3', 'ZCCHC10', YS', 'PER3', 'ALKAL2', 'CPLX1', 'TTLL10', 'TPSB2', 'STMN3', and / or 'EP400P1'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has moderate ulcerative colitis as compared to a sample from a patient who is in remission from ulcerative colitis: 'SIDTl', 'ARHGAP33', 'KDM1A', 'RUBCNL', 'MYB', 'SDC2', H0XC8', 'LINC00661', 'RPS6KA2', 'DMRTB1', 'SPRED3', 'TMEM143', 'MEX3A', 'LOC643339', 'MAPK15', 'MEGF6', and / or 'E2F3'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has moderate ulcerative colitis as compared to a sample from a patient who has severe ulcerative colitis: 'HPSE', 'ANGPTL4', HSPB2-C1 lorf52', 'IFI27L2', 'KLHL22', 'MARVELD3', 'ADRB1', 'NCOA7-AS1', 'LINC00539', 'ADAMTS14', 'EIF4E1B', HIVEP2', 'FAAP20', 'ZNF558', 'APCDD1L', 'EFCAB2', 'LOC105374338', 'TBX15', HIF3A', 'LDB2', 'MY018B', 'CDKN2B-AS1', 'MAB21L2', 'SNCB', 'NM_001371417', 'Clorfl59', 'CPLX1', HES3', 'BRSK1', 'LOC107986163', 'GFI1B', 'SLC22A18AS', 'ALKBH7', 'IKZF2', 'MS4A10', 'CTTN', 'EXPH5', 'NRBF2', 'LRRN1', 'CALM1', 'ERICH6-AS1', 'CDKN2A', 'CNTNAP1', 'APCDD1', 'EXOC2', 'LINC00706', 'PDGFA', 'DNAJB8-AS1', 'BAIAP2L1', and / or 'PCED1B'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who is in remission from ulcerative colitis as compared to a sample from a patient who has severe ulcerative colitis: 'EXOC2', 'IGSF3', 'DNAJB8-AS1', 'DMRTB1', 'PTGIS', 'ECHS1', H0XC8', 'CARMILl', 'MS4A10', 'ANGPTL4', 'HPSE', 'LOC105376453', 'MY018B', 'LINC00706', 'C8orf74', 'ADRB1', 'E2F3', 'KDM1A', 'CDKN2A', 'LOC105374338', 'PDGFA', 'TJP3', 'MDGA2', 'TLCD3B', 'F AMI IOC, 'FAM99B', 'STMN3', 'TBX15', 'NM_001371417', 'GATA3-AS1', 'FAAP20', 'UBE2L5', 'CPNE5', 'IFI27L2', 'KIF25-AS1', 'EFCAB2', 'CUT A', 'CXXC4', 'CDKN2B- AS1', 'MIR6089', 'APCDD1L', 'PIWILr, 'LINC00707', 'CTTN', 'MAPK8IP3', 'RSPH6A', 'CD99P1', 'ZNF558', 'LINC00836', and / or 'ARFGEF2'. In some embodiments, one or more of thefollowing genes may be relatively enriched or relatively depleted in a patient sample for a patient who has mild Crohn’s disease as compared to a sample from a patient who has moderate Crohn’s disease: 'FGF6' and / or 'POP7'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has mild Crohn’s disease as compared to a sample from a patient who is in remission from Crohn’s disease: 'ST8SIA2', 'TNKS1BPT, and / or 'POP7'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has mild Crohn’s disease as compared to a sample from a patient who has severe Crohn’s disease: 'LPCAT2', 'AADACL3', 'DPYSL5', 'TDRP', 'SOX11', 'HSPB9', 'LOCI 00240728', 'FGF6', 'TOR1A', 'SHISA5', 'PRSS38', 'SLCO2A1', 'MIR378I', 'GAL3ST4', 'LOC101929243', 'MARVELD3', 'SLC12A7', 'CLIP3', 'MUC12', 'PRDM12', 'ILRUN', 'UBE2E2', 'KPTN', 'AMDHD2', 'NOVAI', and / or 'SMYD4'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has moderate Crohn’s disease as compared to a sample from a patient who is in remission from Crohn’s disease: 'MUC12', 'NAA40', UBE2E2-AS1', 'MHENCR', and / or 'UBE2E2'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who has moderate Crohn’s disease as compared to a sample from a patient who has severe Crohn’s disease: 'SOX11', 'PRSS38', 'SLCO2A1', 'AMDHD2', 'CLEC4G', 'ST8SIA2', 'LOC101929243', 'AADACL3', 'RAB1A', 'SCNM1', 'SHISA5', 'MIR378I', and 'KPTN'. In some embodiments, one or more of the following genes may be relatively enriched or relatively depleted in a patient sample for a patient who is in remission from Crohn’s disease as compared to a sample from a patient who has severe Crohn’s disease: 'ST8SIA2', 'CLIP3', 'LOC 101929243', 'AMDHD2', 'GAL3ST4', 'UBE2E2', 'RABI A', 'SMYD4', 'MUC12', 'KPTN', 'PRDM12', UBE2E2-AS1', 'AADACL3', 'PRSS38', 'ILRUN', 'TDRP', 'TOR1A', 'ZSWIM4', 'CLEC4G', 'SLC12A7', 'MAPK8IP3', 'SLCO2A1', 'MIR378I', 'NOVAI', 'NAA40', 'LOC 100240728', 'SHISA5', 'DPYSL5', 'MHENCR', HSPB9', 'TNKS1BP1', 'SCNM1', 'MARVELD3', 'SOX11', 'FGF6', and / or 'LPCAT2'.

[0149] In some embodiments, one or more of the following genes may be relatively enriched in a patient sample for a patient who has ulcerative colitis: 'C3', 'SNURF', 'SNRPN', 'NM_001371415', 'ACE2', 'TMEM259', 'FANCF', 'C21orf62-ASl', 'STXBP1', 'ZCCHC10', 'ZNF148', 'PAXBP1', 'AIF1', 'POFUT2', 'SCAT1', 'LINC00205', 'MMGT1', 'SIGLEC15', 'SNAPC4', 'LINC01970', 'C8orf58', 'NR2F1-AS1', 'AURKC, 'CCDC120', 'KIF9', 'TESMIN', 'WDR26', 'NR2F1', 'PLXNB2', 'PXDN', 'KCNQ2', 'BAIAP2L1', 'CST3', 'SYCE3', 'ECHS1', 'UNC80', 'PNKD', 'CRYBB2', 'KIF25-AST, 'TSPYL2', 'CELF4', HAR1B', HTT', 'ASF1B', 'ERG', 'LOC105372633','TMEM164', 'PLEKHG3', 'LAMT0R4', 'FAM221B', 'PDGFA', HRAT92', 'ELM02', 'JPH4', 'NM_OO 1371249', 'LOC105374338', 'CHIC1', 'BMS1P14', 'TICAM1', 'TNIP2', 'CROCC, 'EDF1', HOMEZ', 'PLCXD1', 'SNUPN', 'WFIKKN1', 'TDRD12', 'HAST, 'EXOC2', 'PTK2', 'ASAP3', 'C19orf38', 'UROC1', 'LINC02575', 'TBCC, 'CDKN2A', 'BRD3OS', 'CDKN2B-AS1', 'DCUN1D4', 'MYH16', 'DRP2', 'GPR139', 'CYP2A6', 'SGCA', 'OPTN', 'SBK3', and 'ISL2'. In some embodiments, one or more of the following genes may be relatively enriched in a patient sample for a patient who has ulcerative colitis: 'C3', 'SNURF', 'NM_001371415', 'ACE2', and / or 'TMEM259'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has ulcerative colitis: 'GPIHBPr, 'SLC6A4', 'ZCWPWT, 'FENDRR', 'FAM155A', 'MS4A10', 'AGR3', 'GPR139', and 'CYP2A6'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has ulcerative colitis: 'LINC00482', 'NR2F1', 'FENDRR', 'APOH', and / or 'SLC6A4'. In some embodiments, one or more of the following genes may be relatively enriched in a patient sample for a patient who has mild ulcerative colitis: 'RHO', 'CASC4', 'KLK9', 'HSPA12B', 'NM_001371415', 'LEF', 'RTN4RL1', 'MAML3', 'FLCN', 'MIA3', 'CRYBB2', 'LOCI 12268114', 'CHST3', 'C3', 'ACE2', 'OLIG2', 'SDC2', 'FBXO3', 'MAGEF1', 'FBXO3-DT', 'MIR7-3HG', 'MIR212', 'ASGR2', 'TMEM259', 'PAPP A', 'ANKRD36BP2', 'CCDC120', 'EIF2AK2', 'RSPH6A', 'EDNRB', 'LOCI 00287015', 'PTGIS', 'GMNC, 'MCPH1', 'MIR451B', 'RPS6KA2', 'ASH1L', 'LINC00955', 'SGCA', 'VWF', 'LOC91370', 'GDPD5', 'FBXO27', 'F AMI IOC, 'GFI1B', 'IFI27L2', 'KLHL22', 'CARMIL1', 'NOVAI', 'EXOC2', 'CDKN2A', 'HPSE', 'COLECI 1', HIVEP2', 'OSER1', 'SNCB', 'C6orfl32', 'ANGPTL4', 'CDKN2B-AS1', 'LOC105376453', 'C19orf81', 'GPR182', 'CHMP1A', 'SURF2', HCK', 'CNTNAP1', 'JRK', 'NCOA7-AS1', 'ADRB1', 'FAAP20', 'EIF4E1B', 'SEL1L3', HOXC8', 'CTTN', 'FBXW4', 'R3HDM4', 'BAIAP2L1', 'LINC01970', 'ZNF677', 'SBK3', 'ZCCHC10', 'PER3', 'ALKAL2', 'CPLX1', 'STMN3', 'EP400P1', 'SPRED3', 'MEX3A', 'LOC643339', 'MAPK15', 'MEGF6', 'E2F3', HSPB2-C1 lorf52', 'MARVELD3', 'LINC00539', 'ZNF558', 'APCDD1L', 'EFCAB2', 'LOC105374338', HIF3A', 'LDB2', 'MAB21L2', 'Clorfl59', 'HES3', 'BRSK1', 'LOC107986163', and 'ALKBH7'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has mild ulcerative colitis: HCN2', 'LINC01410', 'MBNL3', 'PUS1', 'LTBP3', 'TBX10', 'RUBCNL', 'KANK2', 'ARHGEF18', 'SUOX', 'LRMDA', 'RAB44', 'AHCY', 'SIDT1', 'SLC22A18AS', 'IKZF2', and 'MS4A10'. In some embodiments, one or more of the following genes may be relatively enriched in a patient sample for a patient who has moderate ulcerative colitis: 'RHO', 'CASC4', 'KLK9', HSPA12B', 'NM 001371415', 'LIF', 'RTN4RLF, 'MAML3', 'FLCN', 'MIA3', 'CRYBB2', 'LOCI 12268114', 'CHST3', 'C3', 'ACE2', 'OLIG2', 'SDC2', 'FBXO3', 'MAGEF1', 'FBXO3-DT',MIR7-3HG', MIR212', 'ASGR2', 'TMEM259', 'PAPPA', 'ANKRD36BP2', 'CCDC120', 'EIF2AK2', 'RSPH6A', 'EDNRB', 'LOCI 00287015', 'PTGIS', 'GMNC', 'MCPH1', MIR451B', 'RPS6KA2', 'ASH1L', 'LINC00955', 'SGCA', 'VWF', 'LOC91370', 'GDPD5', 'FBXO27', 'F AMI IOC, 'GFI1B', 'IFI27L2', 'KLHL22', 'CARMILl', 'NOVA1', 'EXOC2', 'CDKN2A', 'HPSE, 'COLECI 1', HIVEP2', 'OSER1', 'SNCB', 'C6orfl32', 'ANGPTL4', 'CDKN2B-AS1', 'LOC105376453', 'C19orf81', 'GPR182', 'CHMP1A', 'SURF2', HCK', 'CNTNAP1', 'JRK', 'NCOA7-AS1', 'ADRB1', 'FAAP20', 'EIF4E1B', 'SEL1L3', HOXC8', 'CTTN', 'FBXW4', 'R3HDM4', 'BAIAP2L1', 'LINC01970', 'ZNF677', 'SBK3', 'ZCCHC10', 'PER3', 'ALKAL2', 'CPLX1', 'STMN3', 'EP400P1', 'SPRED3', 'MEX3A', 'LOC643339', 'MAPK15', 'MEGF6', 'E2F3', HSPB2-C1 lorf52', MARVELD3', 'LINC00539', 'ZNF558', 'APCDD1L', 'EFCAB2', 'LOC105374338', HIF3A', 'LDB2', MAB21L2', 'Clorfl59', HES3', 'BRSK1', 'LOC107986163', and 'ALKBH7'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has moderate ulcerative colitis: 'HCN2', 'LINC01410', MBNL3', 'PUS1', 'LTBP3', 'TBX10', 'RUBCNL', 'KANK2', 'ARHGEF18', 'SUOX', 'LRMDA', 'RAB44', 'AHCY', 'SIDT1', 'SLC22A18AS', 'IKZF2', and MS4A10'. In some embodiments, one or more of the following genes may be relatively enriched in a patient sample for a patient who has ulcerative colitis in remission: 'RHO', 'CASC4', 'KLK9', 'HSPA12B', 'NM_001371415', 'LIF', 'RTN4RL1', MAML3', 'FLCN', 'MIA3', 'CRYBB2', 'LOCI 12268114', 'CHST3', 'C3', 'ACE2', 'OLIG2', 'SDC2', 'FBXO3', MAGEF1', 'FBXO3-DT', 'MIR7-3HG', MIR212', 'ASGR2', 'TMEM259', 'PAPPA', 'ANKRD36BP2', 'CCDC120', 'EIF2AK2', 'RSPH6A', 'EDNRB', 'LOCI 00287015', 'PTGIS', 'GMNC, MCPH1', MIR451B', 'RPS6KA2', 'ASH1L', 'LINC00955', 'SGCA', 'VWF', 'LOC91370', 'GDPD5', 'FBXO27', 'F AMI 10C, 'GFI1B', 'IFI27L2', 'KLHL22', 'CARMILl', 'NOVAI', 'EXOC2', 'CDKN2A', 'HPSE', 'COLECI 1', HIVEP2', 'OSER1', 'SNCB', 'C6orfl32', 'ANGPTL4', 'CDKN2B-AS1', 'LOC105376453', 'C19orf81', 'GPR182', 'CHMP1A', 'SURF2', 'HCK', 'CNTNAP1', 'JRK', 'NCOA7-AS1', 'ADRB1', 'FAAP20', 'EIF4E1B', 'SEL1L3', HOXC8', 'CTTN', 'FBXW4', 'R3HDM4', 'BAIAP2L1', 'LINC01970', 'ZNF677', 'SBK3', 'ZCCHC10', 'PER3', 'ALKAL2', 'CPLX1', 'STMN3', 'EP400P1', 'SPRED3', MEX3A', 'LOC643339', MAPK15', MEGF6', 'E2F3', HSPB2-C1 lorf52', MARVELD3', 'LINC00539', 'ZNF558', 'APCDD1L', 'EFCAB2', 'LOC105374338', HIF3A', 'LDB2', MAB21L2', 'Clorfl59', HES3', 'BRSK1', 'LOC107986163', and 'ALKBH7'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has ulcerative colitis in remission: HCN2', 'LINC01410', MBNL3', 'PUS1', 'LTBP3', 'TBX10', 'RUBCNL', 'KANK2', 'ARHGEF18', 'SUOX', 'LRMDA', 'RAB44', 'AHCY', 'SIDT1', 'SLC22A18AS', 'IKZF2', MS4A10'. In some embodiments, one or more of the following genes may be relatively enrichedin a patient sample for a patient who has severe ulcerative colitis: 'RHO', 'CASC4', 'KLK9', 'HSPA12B', 'NM_001371415', 'LIF', 'RTN4RLF, 'MAML3', 'FLCN', 'MIA3', 'CRYBB2', 'LOCI 12268114', 'CHST3', 'C3', 'ACE2', 'OLIG2', 'SDC2', 'FBXO3', 'MAGEF1', 'FBXO3-DT', 'MIR7-3HG', 'MIR212', 'ASGR2', 'TMEM259', 'PAPPA', 'ANKRD36BP2', 'CCDC120', 'EIF2AK2', 'RSPH6A', 'EDNRB', 'LOCI 00287015', 'PTGIS', 'GMNC', 'MCPH1', 'MIR451B', 'RPS6KA2', 'ASH1L', 'LINC00955', 'SGCA', 'VWF', 'LOC91370', 'GDPD5', 'FBXO27', 'F AMI IOC, 'GFI1B', 'IFI27L2', 'KLHL22', 'CARMILl', 'NOVA1', 'EXOC2', 'CDKN2A', 'HPSE', 'COLECI 1', 'HIVEP2', 'OSER1', 'SNCB', 'C6orfl32', 'ANGPTL4', 'CDKN2B-AS1', 'LOC105376453', 'C19orf81', 'GPR182', 'CHMP1A', 'SURF2', 'HCK', 'CNTNAP1', 'JRK', 'NCOA7-AS1', 'ADRB1', 'FAAP20', 'EIF4E1B', 'SEL1L3', 'HOXC8', 'CTTN', 'FBXW4', 'R3HDM4', 'BAIAP2L1', 'LINC01970', 'ZNF677', 'SBK3', 'ZCCHC10', 'PER3', 'ALKAL2', 'CPLX1', 'STMN3', 'EP400P1', 'SPRED3', 'MEX3A', 'LOC643339', 'MAPK15', 'MEGF6', 'E2F3', 'HSPB2-C1 lorf52', 'MARVELD3', 'LINC00539', 'ZNF558', 'APCDD1L', 'EFCAB2', 'LOC105374338', 'HIF3A', 'LDB2', 'MAB21L2', 'Clorfl59', 'HES3', 'BRSK1', 'LOC107986163', and 'ALKBH7'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has severe ulcerative colitis: 'HCN2', 'LINC01410', 'MBNL3', 'PUS1', 'LTBP3', 'TBX10', 'RUBCNL', 'KANK2', 'ARHGEF18', 'SUOX', 'LRMDA', 'RAB44', 'AHCY', 'SIDTl', 'SLC22A18AS', 'IKZF2', and 'MS4A10'.

[0150] In some embodiments, one or more of the following genes may be relatively enriched in a patient sample for a patient who has Crohn’s disease: 'C3', 'SNURF', 'SNRPN', 'NM_001371415', 'ACE2', 'TMEM259', 'FANCF', 'C21orf62-ASl', 'STXBP1', 'ZCCHC10', 'ZNF148', 'PAXBP1', 'AIF1', 'POFUT2', 'SCAT1', 'LINC00205', 'MMGT1', 'SIGLEC15', 'SNAPC4', 'LINC01970', 'C8orf58', 'NR2F1-AS1', 'AURKC, 'CCDC120', 'KIF9', 'TESMIN', 'WDR26', 'NR2F1', 'PLXNB2', 'PXDN', 'KCNQ2', 'BAIAP2L1', 'CST3', 'SYCE3', 'ECHS1', 'UNC80', 'PNKD', 'CRYBB2', 'KIF25-AS1', 'TSPYL2', 'CELF4', 'HAR1B', 'HTT', 'ASF1B', 'ERG', 'LOC105372633', 'TMEM164', 'PLEKHG3', 'LAMTOR4', 'FAM221B', 'PDGFA', 'HRAT92', 'ELMO2', 'JPH4', 'NM_001371249', 'LOC105374338', 'CHIC1', 'BMS1P14', 'TICAM1', 'TNIP2', 'CROCC, 'EDF1', 'HOMEZ', 'PLCXD1', 'SNUPN', 'WFIKKN1', 'TDRD12', 'HAST, 'EXOC2', 'PTK2', 'ASAP3', 'C19orf38', 'UROC1', 'LINC02575', 'TBCC, 'CDKN2A', 'BRD3OS', 'CDKN2B-AS1', 'DCUN1D4', 'MYH16', 'DRP2', 'GPR139', 'CYP2A6', 'SGCA', 'OPTN', 'SBK3', and 'ISL2'. In some embodiments, one or more of the following genes may be relatively enriched in a patient sample for a patient who has Crohn’s disease: 'C3', 'SNURF', 'SNRPN', 'NM_001371415', and / or 'ACE2'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has Crohn’s disease: 'GPUFBPl', 'SLC6A4', 'ZCWPWT,'FENDRR', 'FAM155A', 'MS4A10', 'AGR3', 'GPR139', and 'CYP2A6'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has Crohn’s disease: 'GPH4BP1', 'SLC6A4', 'ZCWPW1', 'LINC00482', and / or 'FENDRR'. In some embodiments, one or more of the following genes may be relatively enriched in a patient sample for a patient who has mild Crohn’s disease: 'FGF6', 'POP7', 'ST8SIA2', 'TNKS1BP1', 'LPCAT2', 'AADACL3', 'DPYSL5', 'TDRP', 'LOCI 00240728', 'TOR1A', 'SHISA5', 'PRSS38', 'SLCO2A1', 'LOC101929243', 'MARVELD3', 'SLC12A7', 'CLIP3', 'MUC12', 'PRDM12', 'ILRUN', 'UBE2E2', 'KPTN', 'AMDHD2', 'NOVA1', 'SMYD4', 'NAA40', 'UBE2E2-AS1', 'MHENCR', 'RAB1A', 'SCNM1', 'ZSWIM4', and 'MAPK8IP3'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has mild Crohn’s disease: 'SOX11', 'HSPB9', 'MIR378r, 'GAL3ST4', and 'CLEC4G'. In some embodiments, one or more of the following genes may be relatively enriched in a patient sample for a patient who has moderate Crohn’s disease: 'FGF6', 'POP7', 'ST8SIA2', 'TNKS1BP1', 'LPCAT2', 'AADACL3', 'DPYSL5', 'TDRP', 'LOCI 00240728', 'TOR1A', 'SHISA5', 'PRSS38', 'SLCO2A1', 'LOC101929243', 'MARVELD3', 'SLC12A7', 'CLIP3', 'MUC12', 'PRDM12', 'UBE2E2', 'KPTN', 'AMDHD2', 'NOVAI', 'SMYD4', 'NAA40', 'UBE2E2-AS1', 'MHENCR', 'RAB1A', 'SCNM1', 'ZSWIM4', and 'MAPK8IP3'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has moderate Crohn’s disease: 'SOX11', 'HSPB9', 'MIR378r, 'GAL3ST4', and 'CLEC4G'. In some embodiments, one or more of the following genes may be relatively enriched in a patient sample for a patient who has severe Crohn’s disease: 'FGF6', 'POP7', 'ST8SIA2', 'TNKS1BP1', 'LPCAT2', 'AADACL3', 'DPYSL5', 'TDRP', 'LOCI 00240728', 'TOR1A', 'SHISA5', 'PRSS38', 'SLCO2A1', 'LOC101929243', 'MARVELD3', 'SLC12A7', 'CLIP3', 'MUC12', 'PRDM12', 'UBE2E2', 'KPTN', 'AMDHD2', 'NOVAI', 'SMYD4', 'NAA40', 'UBE2E2-AS1', 'MHENCR', 'RAB1A', 'SCNM1', 'ZSWIM4', and 'MAPK8IP3'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has severe Crohn’s disease: 'SOX11', HSPB9', 'MIR378r, 'GAL3ST4', 'and CLEC4G'. In some embodiments, one or more of the following genes may be relatively enriched in a patient sample for a patient who has Crohn’s disease in remission: 'FGF6', 'POP7', 'DPYSL5', 'TDRP', 'LOCI 00240728', 'TOR1A', 'SHISA5', 'PRSS38', 'SLCO2A1', 'LOC101929243', 'MARVELD3', 'SLC12A7', 'CLIP3', 'MUC12', 'PRDM12', 'UBE2E2', 'KPTN', 'AMDHD2', 'NOVAI', 'SMYD4', 'NAA40', 'UBE2E2-AS1', 'MHENCR', 'RAB1A', 'SCNM1', 'ZSWIM4', and 'MAPK8IP3'. In some embodiments, one or more of the following genes may be relatively depleted in a patient sample for a patient who has Crohn’s disease in remission: 'SOX11', HSPB9', 'MIR378I', 'GAL3ST4', and 'CLEC4G'.Detecting or identifying microbes to detect or identify disease

[0151] Disclosed herein in some embodiments is a method of use of a sample (e.g., plasma) comprising cell-free DNA (mcfDNA) as a means to detect or identify inflammatory bowel disease type and severity. In some embodiments, microbial cell-free DNA may be derived from or more microbes. In some embodiments, microbial cell-free DNA may be shorter than human cell-free DNA. In some embodiments, microbial cell-free DNA may be sequenced to determine abundance of one or more microbes. In some embodiments, microbial cell-free DNA may be sequenced to generate sequence reads. In some embodiments, sequence reads generated from microbial cell- free DNA may be mapped onto one or more reference genomes. In some embodiments, mapping of sequence reads generated from microbial cell-free DNA may be used to identify one or more microbes. In some embodiments, differential abundance analysis may be performed on data generated from analysis of sequence reads derived from microbial cell-free DNA. In some embodiments, differential abundance analysis may compare groups of interest. In some embodiments, groups of interest may comprise subjects in disease remission, subjects with mild disease, subjects with moderate disease, subjects with severe disease, and / or healthy subjects. In some embodiments, effect size may be determined after differential abundance analysis is performed. In some embodiments, one or more microbial features may be selected according to effect size. In some embodiments, one or more microbial features may comprise one or more taxonomic ranks. In some embodiments, one or more microbial features may comprise but are not limited to: species, genus, family, order, class, order, phylum, and kingdom. In some embodiments, additional analysis may be performed using machine learning. In some embodiments, machine learning may comprise the use of a machine-learning classifier or a trained algorithm. In some embodiments, performance of a machine-learning classifier as disclosed herein may be assessed using a 10-fold cross-validation. In some embodiments, a 10-fold cross-validation may be performed multiple times across different partitions. In some embodiments, a 10-fold cross- validation may comprise a leave one clinical site out (LOSO) strategy.

[0152] Provided herein are methods and compositions for detecting or identifying an IBD according to an imbalance of one or more microbes. In some embodiments, IBD may result from the presence of or imbalance in an amount of one or more microbes in a subject. In some embodiments, an imbalance in an amount of one or more microbes in a subject may comprise a statistically significant difference in detection of the one or more microbes relative to a control sample. In some embodiments, one or more microbes may include but are not limited to: Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides vulgatus, Firmicutes, Faecalibacterium prausnitzii, Clostridium, Clostridium leptum, Clostridium difficile, Roseburiahominis, Eubacterium rectale, Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium bifidum, Bifidobacterium adolescentis, Streptococcus thermophilus, Escherichia coli, Enterococcus faecalis, Enterococcus faecium, Fusobacterium nucleatum, Prevotella copri, Prevotella histicola, Ruminococcus bromii, Ruminococcus torques, Parabacteroides distasonis, Akkermansia muciniphila, Veillonella parvula, Coprococcus catus, Dialister invisus, Collinsella aerofaciens, Dorea formicigenerans, Malassezia restricta, Acinetobacter baumannii, Streptococcus sanguinis, Lactobacillus plantarum, Lactobacillus crispatus, Acetobacter ghanensis, an Acetobacter pasteurianus, an Achromobacter ruhlandii, an Achromobacter xylosoxidans, an Acidaminococcus intestini, an Acidovorax avenae, an Acidovorax sp. JS42, an Acidovorax sp. SD340, an Acinetobacter baumannii, an Acinetobacter bereziniae, an Acinetobacter guillouiae, an Acinetobacter harbinensis, an Acinetobacter johnsonii, an Acinetobacter junii, an Acinetobacter Iwoffii, an Acinetobacter nosocomialis, an Acinetobacter sp. PT1, an Acinetobacter ursingii, an Actinomyces graevenitzii, an Actinomyces johnsonii, an Actinomyces oris, an Actinomyces sp. ICM47, an Actinomyces sp. ICM58, an Actinomyces sp. oral taxon 170, an Actinomyces sp. oral taxon 172, an Actinomyces sp. oral taxon 175, an Actinomyces sp. oral taxon 448, an Actinomyces viscosus, an Aeribacillus pallidus, an Afipia broomeae, an Afipia sp. NBIMC P1-C1, an Afipia sp. 0HSU I-C6, an Aggregatibacter aphrophilus, an Aggregatibacter segnis, an Aggregatibacter sp. oral taxon 458, an Agrobacterium sp. SUL3, an Alicycliphilus sp. Bl, an Alicyclobacillus acidocaldarius, an Alloprevotella rava, an Alloprevotella sp. oral taxon 473, an Alloprevotella tannerae, an Alternaria alternata, an Anaerobutyricum hallii, an Anaerococcus obesiensis, an Anaerostipes hadrus, an Anoxybacillus ayderensis, an Anoxybacillus flavithermus, an Anoxybacillus gonensis, an Aquabacterium parvum, an Aspergillus niger, an Aspergillus sydowii, an Aureobasidium pullulans, an Avian endogenous retrovirus EA V-HP, an Azospira oryzae, a Bacillus licheniformis, a Bacillus smithii, a Bacillus subtilis, a Bacteroides caccae, a Bacteroides cellulosilyticus, a Bacteroides finegoldii, a Bacteroides fragilis, a Bacteroides graminisolvens, a Bacteroides ovatus, a Bacteroides stercoris, a Bacteroides thetaiotaomicron, a Bacteroides uniformis, a Bacteroides xylani solvens, a Bacteroidetes bacterium OLBIO, a Bacteroidetes oral taxon 274, a Bifidobacterium adolescentis, a Bifidobacterium minimum, a Bifidobacterium thermacidophilum, a Bilophila wadsworthia, a Blautia hansenii, a Blautia obeum, a Blautia producta, a Blautia sp. KLE 1732, a Blautia wexlerae, a Bradyrhizobium cosmicum, a Bradyrhizobium elkanii, a Bradyrhizobium embrapense, a Bradyrhizobium japonicum, a Bradyrhizobium pachyrhizi, a Bradyrhizobium sp. 17-4, a Bradyrhizobium sp. BTAil, a Bradyrhizobium sp. Leaf 396, a Bradyrhizobium sp. YR681, a Bradyrhizobium viridifuturi, a Brevibacterium mcbrellneri, a Brevundimonas sp. KM4, aBrevundimonas vesicularis, a Brochothrix thermosphacta, a Brucella anthropi, a Brussowvirus bv2972, a Burkholderia contaminans, a Burkholderia vietnamiensis, a Caldibacillus debilis, a Caldibacillus thermoamylovorans, a Campylobacter concisus, a Campylobacter gracilis, a Campylobacter showae, a Candida tropicalis, a Candidatus Methylopumilus planktonicus, a Capnocytophaga gingivalis, a Capnocytophaga granulosa, a Capnocytophaga ochracea, a Capnocytophaga sp. CM59, a Capnocytophaga sp. oral taxon 329, a Capnocytophaga sp. oral taxon 332, a Capnocytophaga sputigena, a Cardiobacterium hominis, a Carnobacterium maltaromaticum, a Catonella morbi, a Ceduovirus bIL67, a Ceduovirus c2, a Chryseobacterium indologenes, a Citrobacter freundii, a Clostridia bacterium UC5.1-1D10, a Clostridia bacterium UC5.1-2H11, a Clostridiales bacterium KLE1615, a Clostridiales bacterium VE202-03, a Clostridiales bacterium VE202-07, a Clostridioides difficile, a Clostridium butyricum, a Clostridium celatum, a Clostridium paraputrificum, a Clostridium perfringens, a Clostridium sp. 1 1 41A1FAA, a Clostridium sp. 7 3 54FAA, a Comamonas aquatica, a Comamonas testosteroni, a Coprococcus sp. HPP0048, a Coprococcus sp. HPP0074, a Corynebacterium accolens, a Corynebacterium afermentans, a Corynebacterium aurimucosum, a Corynebacterium kroppenstedtii, a Corynebacterium matruchotii, a Corynebacterium minutissimum, a Corynebacterium nuruki, a Corynebacterium pseudodiphtheriticum, a Corynebacterium pseudogenitalium, a Corynebacterium sp. KPL1818, a Corynebacterium sp. KPL1859, a Cupriavidus pauculus, a Curvibacter delicatus, a Cutibacterium acnes, a Cutibacterium namnetense, a Cyberlindnera jadinii, a Debaryomyces hansenii, a Deinococcus wulumuqiensis, a Delftia acidovorans, a Delftia lacustris, a Delftia sp. ZNC0008, a Delftia tsuruhatensis, a Dermabacter vaginalis, a Dermacoccus nishinomiyaensis, a Dermacoccus sp. PE3, a Diaphorobacter nitroreducens, a Diaphorobacter sp. J5-51, a Dorea longicatena, an Eikenella corrodens, an Eimeria mitis, an Empedobacter falsenii, an Enhydrobacter aerosaccus, an Enter obacter cloacae, an Enterobacter hormaechei, an Enterobacter sp. BIDMC 27, an Enter obacter sp. BIDMC 109, an Enterobacter sp. BIDMC87, an Enterobacter sp. BIDMC93, an Enterobacter sp. BWH64, an Enterobacter sp. MGH120, an Enterocloster clostridioformis, an Enterococcus cecorum, an Enterococcus italicus, an Escherichia coli, an Escherichia phage HK630, an Escherichia phage T7, an Eubacterium ramulus, an Exophiala oligosperma, a Facklamia hominis, a Faecalibacterium prausnitzii, a Filifactor alocis, a Finegoldia magna, a Flavonifractor plautii, a Francisella tularensis, a Fructilactobacillus sanfranciscensis, a Fusarium graminearum, a Fusobacterium hwasookii, a Fusobacterium nucleatum, a Fusobacterium periodonticum, a Gemella haemolysans, a Gemella morbillorum, a Gemella sanguinis, a Geobacillus sp. Sah69, a Geobacillus sp. WCH70, a Geobacillus stearothermophilus,a Gordonia bronchialis, a Haemophilus haemolyticus, a Haemophilus influenzae, a Haemophilus parahaemolyticus, a Haemophilus parainjluenzae, a Haemophilus paraphrohaemolyticus, a Haemophilus quentini, a Haemophilus sputorum, a Hoylesella nanceiensis, a Hoylesella oralis, a Hoylesella pleuritidis, a Hoylesella shahii, a Human betaherpesvirus 7, a Human gammaherpesvirus 4, a Human immunodeficiency virus 1, a Hungatella hathewayi, an Intestinibacter bartlettii, a Janibacter melonis, a Kingella oralis, a Kitasatospora arboriphila, a Klebsiella michiganensis, a Klebsiella oxytoca, a Klebsiella pneumoniae, a Klebsiella variicola, a Kluyvera intermedia, a Kocuria polaris, a Kocuria rhizophila, a Lachnoanaerobaculum saburreum, a Lachnospira eligens, a Lachnospiraceae bacterium 3 1 46FAA, a Lachnospiraceae bacterium 5 1 57FAA, a Lachnospiraceae bacterium 6 1 37FAA, a Lachnospiraceae bacterium 6 1 63FAA, a Lachnospiraceae bacterium 7 1 58FAA, a Lachnospiraceae bacterium 8 1 57FAA, a Lachnospiraceae bacterium 9 1 43BFAA, a Lacticaseibacillus casei, a Lactiplantibacillus plantarum, a Lactobacillus amylovorus, a Lactobacillus crispatus, a Lactobacillus delbrueckii, a Lactobacillus gallinarum, a Lactobacillus gasseri, a Lactobacillus helveticus, a Lactococcus garvieae, a Lactococcus lactis, a Lactococcus phage BM13, a Lactococcus phage P 335, a Lactococcus phage P 680, a Lactococcus phage bIL310, a Lactococcus phage jm2, a Lachnospira eligens, a Lachnospiraceae bacterium 3 1 46FAA, a Lachnospiraceae bacterium 5 1 57FAA, a Lachnospiraceae bacterium 6 1 37FAA, a Lachnospiraceae bacterium 6 1 63FAA, a Lachnospiraceae bacterium 7 1 58FAA, a Lachnospiraceae bacterium 8 1 57FAA, a Lachnospiraceae bacterium 9 1 43BFAA, a Lacticaseibacillus casei, a Lactiplantibacillus plantarum, a Lactobacillus amylovorus, a Lactobacillus crispatus, a Lactobacillus delbrueckii, a Lactobacillus gallinarum, a Lactobacillus gasseri, a Lactobacillus helveticus, a Lactococcus garvieae, a Lactococcus lactis, a Lactococcus phage BM13, a Lactococcus phage P 335, a Lactococcus phage P 680, a Lactococcus phage bIL310, a Lactococcus phage jm2, a Lactococcus phage jm3, a Lactococcus phage phiLC3, a Lambdavirus lambda, a Lancefieldella parvula, a Lautropia mirabilis, a Leptospira wolffii, a Leptotrichia buccalis, a Leptotrichia shahii, a Leptotrichia sp. oral taxon 215, a Leuconostoc gelidum, a Leuconostoc pseudomesenteroides, a Ligilactobacillus agilis, a Limosilactobacillus fermentum, a Limosilactobacillus reuteri, a Malassezia globosa, a Malassezia restricta, a Malassezia sympodialis, a Mammaliicoccus sciuri, a Massilia alkalitolerans, a Mediterraneibacter faecis, a Melampsora pinitorqua, a Mesorhizobium sp. L103C105A0, a Mesorhizobium sp. L2C054A000, a Mesorhizobium sp. L2C084A000, a Mesorhizobium sp. L2C089B000, a Mesorhizobium sp. LNHC209A00, a Mesorhizobium sp. LNHC220B00, a Mesorhizobium sp. LNHC229A00, a Mesorhizobium sp. LNHC252B00, a Mesorhizobium sp. LNJC384A00, a Mesorhizobium sp.LNJC405B00, a Mesorhizobium sp. LSHC412B00, a Mesorhizobium sp. LSHC420B00, a Mesorhizobium sp. LSHC432A00, a Mesorhizobium sp. LSJC268A00, a Mesorhizobium sp. LSJC269B00, a Mesorhizobium sp. LSJC277A00, a Methanosarcina sp. 1.H. T.1A.1, a Methanosarcina sp. 2.H. T.1A.15, a Methylobacterium sp. Leaf361, a Methylorubrum populi, a Me thy lover satilis universalis, a Microbacterium maritypicum, a Microbacterium oxydans, a Microbacterium sp. H83, a Micrococcus aloever ae, a Micrococcus luteus, a Micrococcus sp. CH 3, a Micrococcus sp. MS-ASIII-49, aModestobacter marinus, a Moineauvirus Abc2, a Moineauvirus DTI, aMoraxella catarrhalis, aMoraxella osloensis, aMorococcus cerebrosus, a Mycobacterium gastri, a Mycobacterium tuberculosis variant bovis, a Mycolicibacterium mucogenicum, a Mycolicibacterium obuense, a Neisseria cinerea, a Neisseria flavescens, a Neisseria macacae, a Neisseria mucosa, a Neisseria sicca, a Nesterenkonia massiliensis, a Nesterenkonia sp. AN1, a Nesterenkonia sp. JCM 19054, a Neurospora terricola, a Nocardioides sp. Rootl22, a Novosphingobium sp. AAP93, a Novosphingobium subterraneum, an Oribacterium sinus, a Paenibacillus terrigena, a Paenirhodobacter enshiensis, a Pantoea agglomerans, a Pantoea ananatis, a Pantoea dispersa, a Pantoea sp. PSNIH2, a Pantoea sp. aB, a Pantoea vagans, a Parabacteroides distasonis, a Parabacteroides merdae, a Paracoccus sphaerophysae, a Parvimonas micra, a Pediococcus acidilactici, a Pelomonas sp. Root 1217, a Pelomonas sp. Root 1237, a Pelomonas sp. Root 1444, a Pelomonas sp. Root405, a Penicillium paxilli, a Penicillium roqueforti, a Peptostreptococcus stomatis, a Phocaeicola dorei, a Phocaeicola massiliensis, a Phocaeicola vulgatus, a Photobacterium phosphoreum, a Porphyromonas catoniae, a Porphyromonas endodontalis, a Porphyromonas sp. KLE 1280, a Prevotella aurantiaca, a Prevotella baroniae, a Prevotella buccae, a Prevotella conceptionensis, a Prevotella denticola, a Prevotella histicola, a Prevotella intermedia, a Prevotella jejuni, a Prevotella melaninogenica, a Prevotella nigrescens, a Prevotella oris, a Prevotella pallens, a Prevotella salivae, a Prevotella sp. C561, a Prevotella sp. F0091, a Prevotella sp. oral taxon 299, a Prevotella sp. oral taxon 306, a Propionibacterium sp. KPL1844, a Proteus mirabilis, a Pseudacidovorax intermedins, a Pseudomonas aeruginosa, a Pseudomonas brenneri, a Pseudomonas extremaustralis, a Pseudomonas fluorescens, a Pseudomonas fragi, a Pseudomonas mendocina, a Pseudomonas moraviensis, a Pseudomonas oleovorans, a Pseudomonas psychrotolerans, a Pseudomonas putida, a Pseudomonas sp. 313, a Pseudomonas sp. AU 11447, a Pseudomonas sp. NBRC 111130, a Pseudomonas sp. NBRC 111131, a Pseudomonas sp. NBRC 111133, a Pseudomonas sp. P818, a Pseudomonas sp. W15Feb9B, a Pseudomonas toyotomiensis, a Pseudomonas weihenstephanensis, a Pseudoxanthomonas sp. GW2, a Pseudoxanthomonas suwonensis, a Psychrobacter sp. 1501(2011), a Ralstonia insidiosa, a Ralstonia mannitolilytica,a Ralstonia pickettii, a Raoultella planticola, a Rhizobium pusense, a Roseburia faecis, a Roseburia hominis, a Roseburia intestinalis, a Roseburia sp. UNK.MGS-15, a Roseomonas gilardii, a Rothia aeria, a Rothia dentocariosa, a Rothia mucilaginosa, a Ruminococcus sp.5 1 39BFAA, a Saccharomyces cerevisiae, a Schaalia odontolytica, a Selenomonas sp. oral taxon 478, a Severe acute respiratory syndrome-related coronavirus, a Skunavirus ASCC191, a Skunavirus CB13, a Skunavirus CB14, a Skunavirus S14, a Skunavirus bIL170, a Skunavirus bibb29, a Sphingobacterium sp. Agl, a Sphingobacterium sp. T2, a Sphingobium xenophagum, a Sphingomonas elodea, a Sphingomonas sp. Ant Hl 1, a Sphingopyxis sp. HO 57, a Staphylococcus arlettae, a Staphylococcus capitis, a Staphylococcus caprae, a Staphylococcus cohnii, a Staphylococcus epidermidis, a Staphylococcus gallinarum, a Staphylococcus haemolyticus, a Staphylococcus hominis, a Staphylococcus lugdunensis, a Staphylococcus pettenkoferi, a Staphylococcus saprophyticus, a Staphylococcus warneri, a Staphylococcus xylosus, a Stenotrophomonas maltophilia, a Stomatobaculum longum, a Streptococcus agalactiae, a Streptococcus anginosus, a Streptococcus australis, a Streptococcus constellatus, a Streptococcus dysgalactiae, a Streptococcus gordonii, a Streptococcus ilei, a Streptococcus infantarius, a Streptococcus infantis, a Streptococcus intermedins, a Streptococcus lutetiensis, a Streptococcus mitis, a Streptococcus mutans, a Streptococcus oralis, a Streptococcus oralis subsp. tigurinus, a Streptococcus parasanguinis, a Streptococcus parauberis, a Streptococcus peroris, a Streptococcus pneumoniae, a Streptococcus pyogenes, a Streptococcus salivarius, a Streptococcus sanguinis, a Streptococcus sp. 263 SSPC, a Streptococcus sp. 343 SSPC, a Streptococcus sp. A12, a Streptococcus sp. Cl 50, a Streptococcus sp. F0442, a Streptococcus sp. SKI 40, a Streptococcus suis, a Streptococcus thermophilus, a Streptomyces purpurogeneiscleroticus, a Stutzerimonas stutzeri, a Sutterella wadsworthensis, a Tannerella forsythia, a Tepidimonas fonticaldi, a Tepidimonas taiwanensis, a Tepidiphilus thermophilus, a Terrisporobacter othiniensis, a Thermicanus aegyptius, a Thermoanaerobacterium saccharolyticum, a Thermoanaerobacterium thermosaccharolyticum, a Treponema denticola, a Treponema medium, a Treponema socranskii, a Treponema sp. OMZ 838, a Trichuris muris, a Trypanosoma cruzi, a Turicibacter sp. H121, a Veillonella atypica, a Veillonella dispar, a Veillonella parvula, a Veillonella sp. ACPI, a Veillonella sp. HPA0037, a Veillonella tobetsuensis, a Weissella paramesenteroides, a Weizmannia coagulans, a Williamsia muralis, a Williamsia sp. D3, a Winkia neuii, a Xanthomonas campestris, a Xenophilus azovorans, a [Clostridium] innocuum, a [Clostridium] nexile, a [Clostridium] symbiosum, a [Eubacterium] brachy, a [Eubacterium] rectale, a [Eubacterium] sulci, a [Ruminococcus] gnavus, and a [Ruminococcus] torques. In some embodiments, ulcerative colitis may comprise an imbalance in one or more microbes including-n-but not limited to: Propionibactierum acnes, Lactococcus lactis, Haemophilus parainfluenzae, Escherichia Coli, Rothia dentocariosa, Malassezia restricta, Streptococcus thermophilus, Rothia dentocariosa, Malassezia restricta, Actinomyces oris, Klebsiella phage JD18, Klebsiella pneumoniae, Streptococcus aureus, Streptococcus epidermidis, Streptococcus saphrophyticus, Dermacoccus nishinomiyaensis, Acinetobacter baumannii, Streptococcus sanguinis, Lactobacillus plantarum, Lactobacillus crispatus, and any combination thereof. In some embodiments, ulcerative colitis may comprise an imbalance in one or more microbes including but not limited to: Propionibactierum, a Lactococcus, Haemophilus, an Escherichia, a Rothia, a Malassezia, a Streptococcus, a Rothia, a Malassezia, an Actinomyces, a Klebsiella, a Dermacoccus, an Acinetobacter, a Lactobacillus, and any combination thereof. In some embodiments, ulcerative colitis may comprise an imbalance in one or more microbes including but not limited to: an Afipia, a Bifidobacterium, a Brochothrix, a Companilactobacillus, a Coprobacillus, an Escherichia, a Leptospira, a Methylobacterium, aPantoea, a Parasutter ella, a Pichia, a Proteus, a Sphingobacterium, an Achromobacter, an Acinetobacter, an Actinomyces, an Aeribacillus, an Alishewanella, an Alistipes, an Alphacoronavirus, an Alphainfluenzavirus, an Anoxybacillus, an Aureobasidium, a Bacillus, a Betacoronavirus, a Blautia, a Burkholderia, a Caldibacillus, a Caldicellulosiruptor, a Campylobacter, a Capnocytophaga, a Chryseobacterium, a Citrobacter, a Clostridia UnClass UnClass UnClass, a Clostridium, a Collinsella, a Coprococcus, a Cupriavidus, a Cyberlindnera, a Delftia, a Dependoparvovirus, a Dialister, a Duffyella, an Emesvirus, an Enhydrobacter, an Enterobacter, an Eubacteriales Family XIII. Incertae Sedis UnClass, an Eubacteriales UnClass UnClass, an Eubacterium, a Finegoldia, a Francisella, a Geobacillus, an Inovirus, an Intestinibacter, a Kingella, a Klebsiella, a Kocuria, a Lachnoanaerobaculum, a Lachnoclostridium, a Lentivirus, a Leuconostoc, a Mediterraneibacter, a Megasphaera, a Melampsora, a Mesorhizobium, a Methanococcus, a Methanosarcina, a Methanothrix, a Methylorubrum, a Moraxella, a Mycobacterium, a Mycolicibacterium, a Nesterenkonia, an Orthopoxvirus, a Paenibacillus, a Paenirhodobacter, a Paraburkholderia, a Paracoccus, a Pelomonas, a Prevotella, a Pseudomonas, aRalstonia, a Rhodococcus, a Rothia, a Ruminococcus, a Saccharomyces, a Schaalia, a Selenomonas, a Sphingobium, a Sphingomonas, a Staphylococcus, a Stenotrophomonas, a Stomatobaculum, a Stutzerimonas, a Sulfurihydrogenibium, a Sutterella, a Tepidimonas, a Tepidiphilus, a Teseptimavirus, a Thermicanus, a Thermoanaerobacterium, a Thomasclavelia, a Trichuris, a Tyzzerella, a Variovorax, a Veillonella, a Weizmannia, a Williamsia, an Enterococcus, an Alicyclobacillus, a Bacteria UnClass UnClass UnClass UnClass UnClass, a Bradyrhizobium, a Brucella, a Curvibacter, a Dermacoccus, an Elaeophora, a Faecalibacterium, a Flavonifr actor, aHalomonas, a Lachnospira, a Lacticaseibacillus, a Lambdavirus, a Liquorilactobacillus, a Lymphocryptovirus, a Novosphingobium, a Rhizopus, a Rhodopseudomonas, a Roseburia, a Schizosaccharomyces, a Streptomyces, a Tequatrovirus, a Vedamuthuvirus, a Fervidobacterium, a Microbacterium, a Retroviridae UnClass, a Neurospora, a Pseudacidovorax, and any combination thereof. In some embodiments, Crohn’s disease may comprise an imbalance in one or more microbes including but not limited to: Propionibactierum, Lactococcus, Haemophilus, Escherichia, Rothia, Malassezia, Streptococcus, Actinomyces, Klebsiella, Dermacoccus, Acinetobacter, Lactobacillus, and any combination thereof. In some embodiments, Crohn’s disease may comprise an imbalance in one or more microbes including but not limited to: Propionibactierum acnes, Lactococcus lactis, Haemophilus parainfluenzae, Escherichia Coli, Rothia dentocariosa, Malassezia restricta, Streptococcus thermophilus, Rothia dentocariosa, Malassezia restricta, Actinomyces oris, Klebsiella phage JD18, Klebsiella pneumoniae, Streptococcus aureus, Streptococcus epidermidis, Streptococcus saphrophyticus, Dermacoccus nishinomiyaensis, Acinetobacter baumannii, Streptococcus sanguinis, Lactobacillus plantarum, Lactobacillus crispatus, and any combination thereof. In some embodiments, Crohn’s disease may comprise an imbalance in one or more microbes including but not limited to: an Afipia, a Bifidobacterium, a Brochothrix, a Companilactobacillus, a Coprobacillus, an Escherichia, a Leptospira, a Methylobacterium, a Pantoea, a Parasutterella, a Pichia, a Proteus, a Sphingobacterium, an Achromobacter, an Acinetobacter, an Actinomyces, an Aeribacillus, an Alishewanella, an Alistipes, an Alphacoronavirus, an Alphainfluenzavirus, an Anoxybacillus, an Aureobasidium, a Bacillus, a Betacoronavirus, a Blautia, a Burkholderia, a Caldibacillus, a Caldicellulosiruptor, a Campylobacter, a Capnocytophaga, a Chryseobacterium, a Citrobacter, a Clostridia UnClass UnClass UnClass, a Clostridium, a Collinsella, a Coprococcus, a Cupriavidus, a Cyberlindnera, a Delftia, a Dependoparvovirus, a Dialister, a Duffyella, an Emesvirus, an Enhydrobacter, an Enterobacter, an Eubacteriales Family XIII. Incertae Sedis UnClass, an Eubacteriales UnClass UnClass, an Eubacterium, a Finegoldia, a Francisella, a Geobacillus, an Inovirus, an Intestinibacter, a Kingella, a Klebsiella, a Kocuria, a Lachnoanaerobaculum, a Lachnoclostridium, a Lentivirus, a Leuconostoc, a Mediterraneibacter, a Megasphaera, a Melampsora, a Mesorhizobium, a Methanococcus, a Methanosarcina, a Methanothrix, a Methylorubrum, a Moraxella, a Mycobacterium, a Mycolicibacterium, a Nesterenkonia, an Orthopoxvirus, a Paenibacillus, a Paenirhodobacter, a Paraburkholderia, a Paracoccus, a Pelomonas, a Prevotella, a Pseudomonas, aRalstonia, a Rhodococcus, a Rothia, a Ruminococcus, a Saccharomyces, a Schaalia, a Selenomonas, a Sphingobium, a Sphingomonas, a Staphylococcus, a Stenotrophomonas, a Stomatobaculum, a Stutzerimonas, aSulfurihydrogenibium, a Sutterella, a Tepidimonas, a Tepidiphilus, a Teseptimavirus, a Thermicanus, a Thermoanaerobacterium, a Thomasclavelia, a Trichuris, a Tyzzerella, a Variovorax, a Veillonella, a Weizmannia, a Williamsia, an Enterococcus, an Alicyclobacillus, a Bacteria UnClass UnClass UnClass UnClass UnClass, a Bradyrhizobium, a Brucella, a Curvibacter, a Dermacoccus, an Elaeophora, a Faecalibacterium, a Flavonifr actor, a Halomonas, a Lachnospira, a Lacticaseibacillus, a Lambdavirus, a Liquorilactobacillus, a Lymphocryptovirus, a Novosphingobium, a Rhizopus, a Rhodopseudomonas, a Roseburia, a Schizosaccharomyces, a Streptomyces, a Tequatrovirus, a Vedamuthuvirus, a Fervidobacterium, a Microbacterium, a Retrovir idae UnClass, a Neurospora, a Pseudacidovorax, and any combination thereof.Combining human and microbial analysis to detect or identify a disease

[0153] Provided herein are methods and compositions for combining data obtained from processing of human cell-free DNA and data obtained from processing of microbial cell-free DNA. In some embodiments, methods disclosed herein may comprise combining analysis of relatively enriched and / or relatively depleted human genes with analysis of an imbalance in one or more microbes to detect or identify a disease. In some embodiments, combining human data obtained from processing of human cell-free DNA and data obtained from processing of microbial cell-free DNA may result in more powerful analysis than analyzing human cell-free DNA alone or microbial cell-free DNA alone. In some embodiments, features determined via analysis of human cell-free DNA and features determined via analysis of microbial cell-free DNA may be fed into a joint classifier or a joint trained algorithm. In some embodiments, a joint classifier may comprise machine learning. In some embodiments, a joint classifier may comprise machine learning and may be trained on input of data obtained from analysis of human cell-free DNA and data obtained from analysis of microbial cell-free DNA. In some embodiments, the machine learning model may take as input data obtained from processing human cell-free DNA concatenated with data obtained from processing microbial cell-free DNA. In some embodiments, the machine learning model may comprise two input channels and take as input data obtained from processing human cell-free DNA in a first input channel and data obtained from processing microbial cell-free DNA in a second input channel.

[0154] Provided herein are methods and compositions for using machine learning to analyze data obtained from processing of human cell-free DNA and data obtained from processing of microbial cell-free DNA. In some embodiments, machine learning may be used to analyze data obtained from processing of human cell-free DNA. In some embodiments, machine learning may be used to analyze data obtained from processing of microbial cell-free DNA. In some embodiments,machine learning may be used to apply findings obtained from analysis of human cell-free DNA to predict findings that may be obtained from analysis of microbial cell-free DNA in a sample or in a subject. In some embodiments, machine learning may be used to apply findings obtained from analysis of microbial cell-free DNA to predict findings that may be obtained from analysis of human cell-free DNA in a sample or in a subject. In some embodiments, machine learning may comprise an extreme gradient boosting (XGBoost) model. In some embodiments, machine learning may comprise a gradient boosted random forest. In some embodiments, machine learning may comprise a random forest. In some embodiments, machine learning may comprise a gradient boosted model. In some embodiments, machine learning may comprise a linear regressor. In some embodiments, machine learning may comprise a logistic regressor. In some embodiments, machine learning may comprise a deep learning model. In some embodiments, machine learning may comprise a decision tree-based method. In some embodiments, machine learning may comprise a supervised learning algorithm. In some embodiments, machine learning may comprise using training data to predict a target variable. In some embodiments, training data may comprise data obtained from processing of human cell-free DNA. In some embodiments, training data may comprise data obtained from processing of microbial cell-free DNA. In some embodiments, machine learning may comprise the use of one or more decision trees. In some embodiments, machine learning may comprise the use of multiple decision trees. In some embodiments, machine learning may comprise one or more generative models. In some embodiments, one or more generative models may be used to generate in silico data. In some embodiments, one or more generative models may be used to expand training data. In some embodiments data may be augmented. In some embodiments, one or more generative models may be used to improve prediction performance of a classifier. In some embodiments, a classifier may comprise use of feature selection. In some embodiments, one or more generative models may be combined with a classifier when using feature selection. In some embodiments, a deep learning model may be developed utilizing in silico data generated using one or more generative models. In some embodiments, a deep learning model developed utilizing in silico data does not use feature selection.

[0155] In some embodiments, performance of a machine-learning classifier as disclosed herein may be assessed using cross-validation. In some embodiments, performance of a machine-learning classifier as disclosed herein may be assessed using a 10-fold cross-validation. In some embodiments, a 10-fold cross-validation may be performed multiple times across different partitions of the dataset. In some embodiments, partitions may be random. In some embodiments, the partitions may be predetermined. In some embodiments the partitions may be predeterminedby the clinical site from which the data in the partitions were obtained. In some embodiments, a 10-fold cross-validation may comprise a leave one clinical site out (LOSO) strategy. In some embodiments, performance of a machine-learning classifier as disclosed herein may be assessed using a greater than 5-fold, 10-fold, or 20-fold cross-validation. In some embodiments, a greater than 5-fold, 10-fold, or 20-fold cross-validation may be performed multiple times across different partitions. In some embodiments, the number of partitions of a dataset, also called folds, may be greater than 5, 10, or 20. In some embodiments, cross-validation may be a leave-one-out cross validation, wherein a single sample is withheld from the training data for assessing validation of the machine learning model. In some embodiments, a greater than 5-fold, 10-fold, or 20-fold cross- validation may comprise a leave one clinical site out (LOSO) strategy. In some embodiments, a cross-validation strategy may comprise analyzing a subset of a dataset to make one or more predictions about a remainder of the dataset. In some embodiments, a cross-validation strategy may comprise analyzing a subset of a dataset to make predictions about a remainder of the dataset until all components of a dataset are predicted upon. In some embodiments, a LOSO strategy may comprise datasets obtained from one or more clinical centers. In some embodiments, a LOSO strategy may comprise training a classifier using data obtained from all but one of the one or more clinical centers to make one or more predictions about the data obtained from the one clinical center not used for training (i.e., the left out clinical center). In some embodiments, a LOSO strategy may be repeated until all clinical sites are predicted upon. In some embodiments, performance of a LOSO strategy across all clinical sites may be aggregated.

[0156] In some embodiments, performance of a machine-learning classifier as disclosed herein may be measured with a performance metric. In some embodiments, a performance metric may comprise at least one of accuracy, sensitivity, specificity, area under the curve (AUC), a receiver operator curve (ROC), Area under the receiver operator curve (AUCROC), f-measure, negative predictive value (NPV), positive predictive value (PPV), or a confusion matrix. In some embodiments, an AUC may be 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or 1. In some embodiments, an AUC may be greater than 0.5, greater than 0.6, greater than 0.7, greater than 0.8, or greater than 0.9. In some embodiments, an AUC may be greater than 0.50, greater than 0.51, greater than 0.52, greater than 0.53, greater than 0.54, greater than 0.55, greater than 0.56, greater than 0.57, greater than 0.58, greater than 0.59, greater than 0.60, greater than 0.61, greater than 0.62, greater than 0.63, greater than 0.64, greater than 0.65, greater than 0.66, greater than 0.67, greater than 0.68, greater than 0.69, greater than 0.70, greater than 0.71, greater than 0.72, greater than 0.73, greater than 0.74, greater than 0.75, greater than 0.76, greater than 0.77, greater than 0.78, greater than 0.79, greater than 0.80, greater than 0.81, greater than 0.82, greater than 0.83, greater than 0.84,greater than 0.85, greater than 0.86, greater than 0.87, greater than 0.88, greater than 0.89, greater than 0.90, greater than 0.91, greater than 0.92, greater than 0.93, greater than 0.94, greater than 0.95, greater than 0.96, greater than 0.97, greater than 0.98, greater than 0.99, or equal to 1.00.Methods of treatment and medical management

[0157] Disclosed herein in some embodiments are methods for treating a subject for an inflammatory disease (e.g., IBD), particularly a sub-type of IBD such as ulcerative colitis (UC) or Crohn’s disease (CD) detected or diagnosed using the methods provided herein. In some embodiments, treating a disease may comprise administering a drug, or performing surgery on the subject. In some cases, medical management of a disease or disorder may also encompass performing an endoscopy on the subject in order to further inform treatment options. As used herein, unless otherwise indicated explicitly, or by context, terms such as “drug,” “medication” and “medicament” are generally used interchangeably.

[0158] In some embodiments, a subject diagnosed using the disclosed methods may be treated with a small molecule drug. In some embodiments, a drug may comprise an aminosalicylate, such as mesalamine, 5-aminosalicylic acid (5-ASA), which can be used to treat UC or CD. In some embodiments, the patient can be treated with a steroid. In some embodiments, a steroid may comprise prednisolone. In some embodiments, ulcerative colitis may comprise steroid-dependent ulcerative colitis. In some embodiments, ulcerative colitis may comprise steroid refractory ulcerative colitis. In some embodiments, drugs that are used to treat steroid-dependent ulcerative colitis may also be used to treat steroid-refractory ulcerative colitis. In some embodiments, thiopurines may be used to treat ulcerative colitis.

[0159] In some embodiments, one or more rapidly effective drugs may be used in subjects with high disease activity. In some embodiments, one or more rapidly effective drugs may comprise but are not limited to JAK inhibitors, TNF antibodies, ustekinumab, and / or tofacitinib. In some embodiments, an antibody drug may comprise but is not limited to one or more of infliximab, golimumab, vedolizumab, and / or mirikizumab. In some embodiments, an effective treatment for mild to moderate UC may be for example 5-aminosalicylic acid. In some embodiments, a moderate to severe UC may be treated with advanced therapies that target specific inflammation pathways. In some embodiments, advanced therapies that target specific inflammation pathways may comprise for example monoclonal antibodies to TNF, a4p7 integrins, and IL-12 and IL-23 cytokines, as well as oral small molecule therapies targeting JAK or sphingosine- 1 -phosphate. In some embodiments, a treatment for Crohn’s disease may comprise but is not limited to one or more of a corticosteroid, an immunosuppressant, a biologic, an antibiotic, an aminosalicylate, and / or a methotrexate. In some embodiments, a treatment for Crohn’s disease may comprise butis not limited to one or more of: medications (such as, for example, 5-ASAs, corticosteroids, immunosuppressants, biologies like TNF inhibitors, integrin inhibitors, JAK inhibitors, antibiotics), corticosteroid enemas, topicals, nutritional therapy (such as, for example, enteral nutrition, TPN, specific diets like low FODMAP), probiotics, prebiotics, surgery (resection, ostomy, strictureplasty), bowel rest, immunomodulators, corticosteroid injections, mesalamine, azathioprine, methotrexate, cyclosporine, tacrolimus, anti-TNF agents (infliximab, adalimumab), anti-integrin therapies (vedolizumab), Janus kinase inhibitors (tofacitinib), fecal microbiota transplantation, fecal transplants, vitamin and / or mineral supplements (B12, D, calcium), alternative therapies (acupuncture, herbal supplements), stress management techniques, physical therapy, smoking cessation, high-fiber diet, low-residue diet, pain management, lifestyle changes (weight management, exercise), vitamin D supplementation, iron supplementation, fluid and electrolyte balance, and / or mesalazine enemas, or any combination thereof.

[0160] Specific treatments can be tailored to the severity and clinical presentation of the subtype of IBD. For example, for mild to mild-moderate ulcerative colitis (UC), 5-ASA medications (e.g., mesalamine, balsalazide, sulfasalazine) can be administered orally and / or rectally, sometimes in combination with a topical steroid (e.g., budesonide foam). For moderate to moderately severe forms of UC, additional treatments can be initiated alone or in combination with existing 5-ASA therapy. In some embodiments, these additional treatments may include systemic corticosteroids (e.g., prednisone), immunomodulators (e.g., azathioprine, 6-MP), biologies (e.g., anti-TNF, anti- integrin agents), or a combination of these therapies. For severe UC, intravenous (IV) or high-dose oral corticosteroids (e.g., IV methylprednisolone) may be required. More aggressive treatments can be added as needed. In some embodiments, these more aggressive treatments may include biologies (e.g., infliximab, adalimumab, golimumab, vedolizumab), immunomodulators (e.g., azathioprine, 6-MP), or calcineurin inhibitors (e.g., cyclosporine, tacrolimus), either alone or in combination.

[0161] As another example, mild to mild-moderate CD, budesonide can be a preferred treatment for mild ileocecal or right-sided CD. Conventional steroids (e.g., prednisone) may be used if budesonide proves inadequate or if the disease is more extensive. Antibiotics (e.g., metronidazole, ciprofloxacin) may be considered in specific cases, particularly for perianal or fistulizing disease (off-label). 5-ASA or sulfasalazine may provide some benefit in mild colonic CD, though they are generally less effective for CD compared to UC. For moderate to moderately severe CD, systemic corticosteroids (e.g., prednisone) are often first-line to control moderate flares. Immunomodulators (e.g., azathioprine, 6-MP, methotrexate) may be introduced for steroid-dependent patients or those with frequent relapses. Biologies may be utilized in cases of inadequate response to steroids orimmunomodulators, or in patients with high-risk features. These include anti-TNF agents (e.g., infliximab, adalimumab, certolizumab pegol), anti-integrin agents (e.g., vedolizumab), or IL-12 / 23 inhibitors (e.g., ustekinumab).

[0162] For severe or complicated CD, high-dose systemic corticosteroids (e.g., IV methylprednisolone) are often required for hospitalized patients. Biologies (e.g., anti-TNF agents, vedolizumab, ustekinumab) may be used alone or in combination with immunomodulators. In refractory cases, calcineurin inhibitors (e.g., cyclosporine, tacrolimus) may be considered, though they are less commonly used in CD compared to UC. Antibiotics are indicated when there is a suspicion of abscesses, fistulas, or perianal complications. Surgery may be necessary for complications such as obstruction, perforation, abscesses that cannot be drained, or massive hemorrhage.

[0163] In some embodiments, certain dosages of medications may be administered to treat mild to moderate inflammatory bowel disease (IBD). In some embodiments, medications for mild to moderate IBD may be used to reduce inflammation. In some embodiments, aminosalicylates (5- ASAs) (such as, for example, mesalamine) may be administered for mild to moderate IBD at a dosage of 1.2 to 4.8 grams per day, divided into 1-3 doses depending on the formulation. In some embodiments, 5-ASAa may be administered orally. In some embodiments, 5-ASAa may be administered as a rectal enema for distal inflammation. In some embodiments, sulfasalazine may be administered for mild to moderate IBD at 2 to 4 grams per day, divided into 2-4 doses. In some embodiments, budesonide may be administered for mild to moderate IBD at 9 mg per day. In some embodiments, a corticosteroid (such as, for example, prednisone) may be administered for mild to moderate IBD at 40 to 60 mg per day. In some embodiments, probiotics (such as, for example, Saccharomyces boulardii) may be administered for mild to moderate IBD at 250-500 mg twice a day. In some embodiments, an antibiotic such as metronidazole may be administered for mild to moderate IBD at 500 mg twice a day or ciprofloxacin may be administered for mild to moderate IBD at 500 mg twice a day.

[0164] In some embodiments, certain dosages of medications may be administered to treat severe inflammatory bowel disease (IBD). In some embodiments, biologies and immunosuppressants may be recommended for severe IBD. In some embodiments, Infliximab may be administered for severe IBD at 5 mg / kg. In some embodiments, Infliximab may be administered at weeks 0, 2, and 6, followed by maintenance doses every 8 weeks. In some embodiments, adalimumab may be administered for severe IBD at 160 mg initially, followed by 80 mg at week 2, then 40 mg every other week. In some embodiments, vedolizumab may be administered for severe IBD at 300 mg at weeks 0, 2, and 6, then every 8 weeks. In some embodiments, immunosuppressants includingbut not limited to azathioprine (1.5-2.5 mg / kg per day) or mercaptopurine (1-1.5 mg / kg per day) may be administered for severe IBD. In some embodiments, surgical options (such as, for example, resection surgery or strictureplasty) may be utilized to manage complications of severe IBD. In some embodiments, Cimzia (certolizumab pegol) may be used to treat Crohn’s disease. In some embodiments, Colazal (balsalazide disodium) may be used to treat ulcerative colitis. In some embodiments, one or more biologic drugs may be used to treat Crohn’s disease and / or ulcerative colitis. In some embodiments, one or more biologic drugs may comprise but are not limited to: Humira (adalimumab), Entyvio (vedolizumab), and Skyrizi (risankizumab).

[0165] Additional non-limiting examples of treatments and dosages that may be used for Crohn’s disease and ulcerative colitis are provided below in Table 1.Table 1: Example drug treatments for IBD

[0166] Medications for IBD may sometimes be used to address variabilities in disease presentation. In some embodiments, dosing of medicaments for Crohn’s disease may require flexibility due to complexity and / or variability of disease presentation. CD can be associated with, in some cases, transmural inflammation, strictures, and / or fistulas. Dosing of medicaments for UC may need to manage mucosal inflammation such as mucosal inflammation localized to the colon. In some embodiments, Crohn’s disease may affect one or more segmental regions of the gastrointestinal tract. In some embodiments, medicaments may be used to target one or more wide areas for treatment of Crohn’s disease. In some embodiments, Crohn’s disease may manifest as a systemic disease. In some embodiments, Crohn’s disease may be treated as a systemic disease. In some embodiments, a personalized treatment plan may be used to treat Crohn’s disease. In some embodiments, a personalized treatment plan may be used to treat ulcerative colitis.

[0167] Provided herein are methods and compositions which may facilitate making a patient diagnosis and / or informing a treatment regimen. The methods and compositions as described herein may be used to distinguish a patient with IBD from a healthy patient. The methods and compositions as described herein may be used to distinguish a patient with IBD from a patient in remission from IBD. The methods and compositions may be further used to differentiate between types and / or subtypes of IBD. The methods and compositions may be further used to differentiate between severities of types and / or subtypes of IBD. In some embodiments, a subject may already have received a diagnosis from a physician. In some embodiments, the diagnosis may be based upon a physical examination, blood test, stool test, imaging study, reported symptoms, medications, personal medical history, family medical history, or any combination thereof. In some embodiments, the subject may have not yet received a diagnosis. In some embodiments, the subject may have received a colonoscopy and / or an endoscopy. In some embodiments, the methods and compositions disclosed herein may facilitate the determination of the need for a targeted colonoscopy and / or a targeted treatment regimen. In some embodiments, the methods and compositions disclosed herein may inform the use of one or more specific drugs and / or dosages of one or more specific drugs to treat an IBD. In some embodiments, the methods and compositions disclosed herein may improve the success of treatment of an IBD. In some embodiments, themethods and compositions disclosed herein may reduce the cost, invasiveness, negative effects, time, and / or efficacy of treatment of an IBD. In some embodiments, the methods disclosed herein may be used to inform the use of a specific surgery for an IBD. In some embodiments, the methods and compositions disclosed herein may reduce the time to reach an accurate diagnosis for an IBD. In some embodiments, the methods and compositions disclosed herein may prevent the development of a severe IBD. In some embodiments, the methods and compositions disclosed herein may shorten the timeline of treating an IBD by at least 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months, 1 year, 2 years, 3 years, 4 years, 5 years, 6 years, or more. In some embodiments, the methods and compositions disclosed herein may inform a monitoring process of an IBD. In some embodiments, the methods and compositions disclosed herein may be used as part of a monitoring process of an IBD. In some embodiments, the methods and compositions disclosed herein may clarify a diagnosis of IBD. In some embodiments, the methods and compositions disclosed herein may clarify a diagnosis of IBD when an endoscopy result is unclear. In some embodiments, the methods and compositions disclosed herein may distinguish a severity of an IBD when a subject’s symptoms are mild. In some embodiments, the methods and compositions disclosed herein may indicate an IBD is moderate or severe when patient symptoms are mild.

[0168] In some embodiments, the methods and compositions herein may inform a treatment regimen for IBD. In some embodiments, a treatment regimen for IBD may begin with an induction phase. In some embodiments, an induction phase may comprise the reduction of symptoms. In some embodiments, the induction phase may achieve remission. In some embodiments, the induction phase may comprise aggressive treatment. In some embodiments, the induction phase may be intended to quickly control inflammation. In some embodiments, a treatment regimen for IBD may comprise a maintenance phase. In some embodiments, the maintenance phase may begin after remission is achieved. In some embodiments, the maintenance phase may be intended to maintain remission, prevent flares, and / or minimize use of corticosteroids. In some embodiments, the maintenance phase may be important for long-term disease management and / or improving quality of life. In some embodiments, a treatment regimen for IBD may comprise transitioning from an induction phase to a maintenance phase. In some embodiments, the transitioning may be personalized to a patient’s response to treatment, side effect profiles of one or more medicaments, and / or disease severity. In some embodiments, the transitioning may comprise tapering off potent induction agents such as but not limited to corticosteroids. In some embodiments, the transitioning may comprise the optimizing of dosages of one or more maintenance medications.

[0169] In some embodiments, the methods and compositions disclosed herein may inform the administration of a first medicament at an initial induction dose. In some embodiments, the subject may receive the first medicament at an initial induction dose before the application of the methods and compositions described herein. In some embodiments, the methods and compositions described herein may inform whether the subject ought to continue receiving the first medicament at the initial induction dose, or whether the dose ought to be reduced or increased, or whether the medicament ought to be discontinued. In some embodiments, the methods and compositions described herein may inform whether a subject ought to receive a second medicament in addition to or in place of the first medicament.

[0170] In some embodiments, the methods and compositions disclosed herein may be repeatedly applied one or more times or may be applied multiple times over the course of a treatment regimen for an IBD. In some embodiments, the methods and compositions disclosed herein may be applied to determine which site to apply a site-specific endoscopy to. In some embodiments, the methods and compositions disclosed herein may reduce the number of endoscopies that a patient may need to receive in order for an IBD for be treated.

[0171] In some embodiments, the methods and compositions disclosed herein may be used to differentiate a first type of IBD and a second type of IBD. In some embodiments, the first type of IBD may be for example associated with inflammatory regions along the entirety of the digestive tract. In some embodiments, the second type of IBD may be for example associated with inflammatory regions localized to the large intestine, the rectum, or both the large intestine and the rectum. In some embodiments, if a first type of IBD is detected, an endoscopic biopsy procedure is performed that targets multiple locations along the entirety of the digestive tract; and if the second type of IBD is detected, an endoscopic biopsy procedure is performed that targets a region limited to the large intestine and the rectum. In some embodiments, an IBD may target one or more regions of a digestive tract. In some embodiments, an IBD may target one or more of an ilium, a large bowel, or both. In some embodiments, an endoscopic procedure may be performed on one or more of an ilium, a large bowel, or both.

[0172] In some cases, a medication is administered orally, intrathecally, or subcutaneously. In some embodiments, a drug may be administered orally. In some embodiments, a drug may be administered rectally, e.g., in the form of a suppository, foam, or enema.

[0173] Patients with a severe subtype of UC or CD can undergo a surgical intervention, especially if the disease is refractory to medication. The direction of the surgery may be dictated by the nature and location of the lesions. Exemplary surgical interventions for UC can include: proctocolectomy (removal of both colon and rectum), particularly for severe forms of UC. In somecases, the surgery also includes removal of the anus and creation of an external ostomy. Exemplary surgical interventions for CD, can include strictureplasty to widen narrowed areas of the intestine caused by strictures, proctocolectomy, colectomy, fistula removal, small and large bowel resection, abscess drainage, and / or ostomy surgery. In some embodiments, the methods provided herein can be used to monitor a patient subsequent to surgery. The monitoring can be used, for example, to determine the efficacy of the surgery and for medication management post-surgery. The monitoring can be performed periodically, e.g., every week, month, three months, six months, or more. If a worsening of disease is revealed during monitoring, the methods may comprise adjusting the medication of the patient or performing an endoscopy to further illuminate the nature of the disease.

[0174] In some embodiments, the methods of diagnosis and detection disclosed herein may be used as a diagnostic to compliment treatments disclosed herein. In some embodiments, methods of combined diagnosis and therapy may include determining the length or duration of therapy, in determining the range of effective dosage, in monitoring a patient’s reaction to changes in treatment, and / or in clinical trials assessing safety or efficacy of a new method of treatment. In some embodiments, disclosed diagnostics can be used before, during, and / or after a treatment phase, including surgery. In some embodiments, disclosed diagnostics can be used in determining a standard of care for a patient or human subject before or during the onset of symptoms of Crohn’s disease, UC, or inflammatory bowel disease. In some embodiments, the methods of diagnosis and detection disclosed herein may inform the use of an intervention. In some embodiments, the methods of diagnosis and detection disclosed herein may inform the use of a surgical intervention. In some embodiments, the methods of diagnosis and detection disclosed herein may inform the use of a therapy. In some embodiments, the methods of diagnosis and detection disclosed herein may inform the use of targeted therapy. In some embodiments, the methods of diagnosis and detection disclosed herein may inform the use of a targeted therapy comprising one or more of a drug, a surgery, a behavioral modification, a lifestyle change, a change in diet, and / or a therapeutic regimen. In some embodiments, the methods disclosed herein may inform a dosage of a drug used. In some embodiments, the methods disclosed herein may be used to inform the administration of an initial induction dose of a drug. In some embodiments, the methods disclosed herein may inform the use of an endoscopic procedure. In some embodiments, the methods disclosed herein may inform the use of a site-specific endoscopy procedure.

[0175] In some embodiments, the methods disclosed herein may guide the selection of the type of endoscopy performed on a subject. The types of endoscopies can include, but are not limited to, ileoscopy, colonoscopy, ileocolonoscopy, sigmoidoscopy, upper endoscopy,esophagogastroduodenoscopy (EGD), capsule endoscopy, or balloon-assisted endoscopy. In some embodiments, an endoscopy procedure (e.g., colonoscopy) may be performed to diagnose or detect a subtype of IBD. Generally, endoscopies can provide a visual image of the intestinal lining that can inform a diagnosis. In some cases, the endoscopy may also be used to biopsy tissue in order to further diagnose the subtype if IBD.

[0176] The decision to perform a specific type of endoscopy is typically based on the patient's symptoms and suspected diagnosis. For example, if a patient presents with symptoms such as diarrhea, weight-loss, and / or abdominal pain and has IBD with an unknown subtype, the clinician may order a colonoscopy and / or ileoscopy in order to determine the precise subtype and location of the inflammation. Often, the first type of endoscopy performed is a colonoscopy in order to look for the contours of inflammation within the intestinal lining of the colon (large intestine and rectum). The clinician may determine that the patient has UC if certain hallmarks of UC are observed, such as continuous regions or bands of inflammation. CD may be diagnosed, if for example, inflamed patches are detected. If during the colonoscopy, the clinician begins to suspect that the subject has CD, an ileoscopy may be needed, which is a more invasive procedure than a colonoscopy. In some cases, the ileoscopy may also require a separate visit. Conversely, if continuous inflammation characteristic of ulcerative colitis (UC) is observed during the colonoscopy, the clinician may decide not to proceed with an ileoscopy.

[0177] In some cases, the IBD can be found to be indeterminate after the endoscopy, depending on the manifestation of the disease or the accessibility of the inflamed region to the scope. For example, continuous patches of inflammation might be consistent with UC, but could also be consistent with a severe CD in which multiple “patches” of inflammation have become interconnected, giving an appearance of continuity. In some other cases, the clinician may not be able to reach the affected areas. For example, the shape or constrictions in the bowel may obstruct the ability of the scope traverse it.

[0178] In some embodiments, the methods disclosed herein can diagnose the subtype of IBD in a non-invasive fashion and avoid certain endoscopic procedures. For example, if the methods provided herein detect that a subject has UC, the clinician can likely plan to just perform a colonoscopy. If the methods provided herein detect CD, the patient may have both a colonoscopy and an ileoscopy during the initial procedure.

[0179] Samples

[0180] Disclosed herein are methods and compositions for processing one or more samples obtained from one or more subjects. In some embodiments, the terms “patient” and “subject” may be used interchangeably. In some embodiments, a sample provided herein may comprise a nucleicacid molecule to be sequenced by a method described herein. As used herein, a “sample” generally refers to any material comprising nucleic acids that has been derived from a subject described herein. A sample may comprise a raw biological sample, such as whole blood. As used herein, the phrase “raw biological sample” refers to an unmanipulated or unprocessed sample obtained from a subject, e.g., a host, containing or presumed to contain target nucleic acids. In some embodiments, a raw biological sample has not been subjected to any extraction methods after being obtained from a subject. In some embodiments, a raw biological sample can be processed or manipulated to produce an initial sample. For example, a raw biological sample may comprise whole blood which is centrifuged to produce an initial sample of plasma for a sequencing assay. As used herein, the term “initial sample” refers to a sample comprising nucleic acids derived from a raw biological sample. In some embodiments, an initial sample may comprise a sample that has been processed or manipulated, such as plasma or serum. In some embodiments, an initial sample may comprise target or desired nucleic acids obtained or extracted from a raw biological sample. In some embodiments, an initial sample can be subj ected to a sequencing assay as described herein. In some embodiments, a raw biological sample or an initial sample can be used directly in a sequencing assay as described herein without extraction of a nucleic acid. In some embodiments, a nucleic acid as described herein can be extracted from a raw biological sample or an initial sample for use in a sequencing assay as described herein. In some embodiments, an extraction method may comprise an alcohol-based extraction, a column purification, a filtration, a size separation, or any combination thereof. As used herein, “removal” or “extraction,” and their cognates, of nucleic acids refers to steps prior to the start of generating or preparing a nucleic acid library that separates nucleic acids from at least one component with which they are normally associated. In some embodiments, removal or extraction of nucleic acids can refer to the process of creating an initial sample from a raw biological sample. For example, without limitation, the fractionation of whole blood into its component parts, such as plasma, can be considered to involve removal or extraction. Similarly, purification or isolation of DNA from a sample (e.g., plasma sample) can be considered extraction. In some embodiments, a nucleic acid extracted from a sample can be subjected to a sequencing assay as described herein. In some embodiments, a raw biological sample or an initial sample may comprise a biological sample.Biological fluids

[0181] In some embodiments, a sample may comprise a biological sample obtained or collected from a subject. In some embodiments, a biological sample may comprise cells. In some embodiments, a biological sample can be substantially cell-free. In some embodiments, a biological sample may comprise a biological fluid. In some embodiments, a biological fluid maycomprise a bodily fluid of a subject (e.g., blood), a fluid obtained from the subject via a medical procedure (e.g., lavage, bronchoalveolar lavage), or any fluid obtained from processing a biopsy of the subject (e.g., serous fluid). In some embodiments, a biological fluid may comprise a bodily fluid. In some embodiments, a bodily fluid may comprise a non-fecal bodily fluid. In some embodiments, a bodily fluid may comprise a whole blood, a plasma, a serum, a lymph, a synovial fluid, a cerebrospinal fluid (CSF), a saliva, a gastric juice, a bile, a pancreatic juice, an intestinal fluid, a respiratory tract mucosal secretion, a semen, a cervical mucus, a vaginal secretion, a urine, a sebum, a breast milk, an amniotic fluid, a pericardial fluid, a pleural fluid, a peritoneal fluid, or any combination thereof. In some embodiments, a biological fluid can be processed from a bodily fluid. For example, blood from a subject can be processed to generate a plasma sample, a serum sample, or a platelet sample. In some embodiments, a biological fluid may comprise a plasma sample. In some embodiments, a biological fluid may comprise a lavage from diagnosing, treating, or cleaning an area of a body of a subject. In some embodiments, a lavage may comprise a bronchoalveolar lavage (BAL), a gastric lavage, a peritoneal lavage, a nasal lavage, a bladder lavage, a rectal lavage, a wound lavage, a joint lavage (arthrocentesis), an eye lavage, a sinus lavage, or any combination thereof. In some embodiments, a biological fluid may comprise an amniotic fluid. In some embodiments, a biological fluid may comprise a BAL. In some embodiments, a biological fluid may comprise a joint lavage. In some embodiments, a biological fluid may comprise a fluid obtained from processing a biopsy of a subject. In some embodiments, a biological fluid may comprise a needle aspiration fluid, a serous fluid, a microdialysis fluid, an exudate fluid, or any combination thereof. As used herein, “plasma” or “blood plasma” refers to the liquid component or fraction of blood. Plasma is generally obtained by spinning a whole blood sample and removing the liquid component.Process control molecules

[0182] As used herein, the phrase “process control molecules” refers to molecules that are added to a sample before or during nucleic acid library generation to aid in the identification or quantification of nucleic acids in a sample. In some embodiments, process control molecules may comprise nucleic acids. In some embodiments, process control molecules may comprise synthetic nucleic acids. In some embodiments, process control molecules are separate from and not integrated in the target molecules. In some embodiments, process control molecules can have special features such as specific sequences, lengths, GC content, degrees of degeneracy, degrees of sequence diversity, different secondary, tertiary, or quaternary structures, and / or known starting concentrations. In some embodiments, process control molecules can be used for normalizing the signal in a sample to account for variations in sample processing or to control process performance.In some embodiments, process control molecules can include sample identifiers. In some embodiments, process control molecules may comprise dephosphorylation control molecules, denaturation control molecules, and / or ligation control molecules. In some embodiments, multiple different types or sets of control molecules can be added to a sample.

[0183] As used herein, the phrase “adapter attachment control molecule” refers to a control molecule that allows monitoring of the efficiency of an adapter attachment reaction. An adapter attachment reaction can be ligation-based, TdT-based, template-switching-based, primer- extension-based, amplification-based, or a combination thereof.

[0184] As used herein, the phrase “degradation assessment molecules” refers to a control molecule used to evaluate sample and spiked sample integrity during processing.

[0185] As used herein, the phrase “spiked initial sample” refers to an initial sample to which process control molecules (or synthetic spike-ins) have been added prior to the start of generating a sequencing library.

[0186] As used herein, “sequence diversity controls” refers to degenerate pools, or pools of nucleic acids with diverse sequences, which degenerate pools can often be used for diversity assessment, abundance calculation, and / or determination of information transfer efficiency /

[0187] As used herein, “size controls,” “length controls,” “GC Spike-in Panel” or “GC size / length controls” refers to nucleic acids that are size or length or GC-content markers, which can be used for abundance normalization, development, and / or analysis purposes and other purposes.

[0188] As used herein, “ID Spike(s)” refers to identification spikes that can be used, for example without limitation, for sample identification tracking, cross-contamination detection, reagent tracking, and / or reagent lot tracking (See, for example, United States patent 9,976,181).Subjects

[0189] Disclosed herein are samples or biological fluids derived from a subject. In some embodiments, samples or biological fluids derived from a subject may comprise nucleic acids. In some embodiments, samples or biological fluids derived from a subject may comprise cell-free nucleic acids. In some embodiments, a subject may comprise a human or a non-human animal. In some embodiments, a subject may comprise a male or a female. In some embodiments, a subject can be of any age. In some embodiments, a subject can be a child. In some embodiments, a subject may comprise an embryo or a fetus. In some embodiments, a subject may comprise but is not limited to Homo sapiens, Caenorhabditis elegans (Nematode), Drosophila melanogaster (Fruit fly), Mus musculus (House mouse), Danio rerio (Zebrafish), Arabidopsis thaliana (Plant model), Xenopus laevis (African clawed frog), Gallus gallus (Chicken), Rattus norvegicus (Rat), Cricetus cricetus (Golden hamster), Schizosaccharomyces pombe (Fission yeast), Tetraodon nigroviridis(Pufferfish), Trichoplax adhaerens (Simple animal), Chlamydomonas reinhardtii (Green alga), Ailuropoda melanoleuca (Giant panda), Panthera leo (Lion), Canis lupus familiaris (Dog), Felis catus (Cat), Bos taurus (Cow), Sus scrofa (Pig), Oryctolagus cuniculus (Rabbit), Equus caballus (Horse), Gallus gallus domesticus (Domestic chicken), Cavia porcellus (Guinea pig), Peromyscus maniculatus (Deer mouse), Cotumix japonica (Japanese quail), Macaca mulatta (Rhesus monkey), Callithrix jacchus (Common marmoset), Spermophilus tridecemlineatus (Thirteen-lined ground squirrel), Tursiops truncatus (Bottlenose dolphin), Pan troglodytes (Chimpanzee), Gorilla gorilla (Gorilla), Pongo pygmaeus (Orangutan), Canis lupus (Wolf), Ursus maritimus (Polar bear), Brachypodium distachyon (Grass model), Ctenophore (Comb jelly), Aplysia californica (Sea slug), Xenopus tropicalis (African clawed frog - another species), Anolis carolinensis (Green anole), Litoria caerulea (Green tree frog), Toxoplasma gondii (Protozoan), Artemia salina (Brine shrimp), Rhipicephalus (Tick), Nereis virens (Marine worm), Opisthorchis viverrini (Liver fluke), Helix aspersa (Garden snail), Heterocephalus glaber (Naked mole-rat), or Fugu rubripes (Pufferfish). In some embodiments, a subject may comprise an animal. In some embodiments, an animal may comprise a vector for disease transmission from which a sample is being tested to determine a presence or absence of a pathogen in the animal. In some embodiments, a disease vector may comprise an animal that has come into contact with a human subject. In some embodiments, an animal coming into contact with a human subject may comprise an animal biting a human, a human ingesting an animal or a secretion of an animal, or a combination thereof. In some embodiments, an animal may comprise a mammal, a bird, a reptile, an amphibian, a fish, an insect, or an arachnid. In some embodiments, an animal may comprise a research animal, an animal for medical use (e.g., xenotransplant donor), a companion animal, a farm animal, a working animal, a performance animal, or a wild animal. In some embodiments, a mammal may comprise a non-human primate (e.g., a macaque or rhesus monkey), a rodent, a carnivore (e.g., a canine or a feline), a bat, a cetacean (e.g., a dolphin), an ungulate, or an insectivore (e.g., a hedgehog). In some embodiments, an ungulate may comprise a swine, a sheep, a cow, a deer, or a horse.

[0190] In some embodiments, a subject may comprise a healthy subject. In some embodiments, a subject can have, be suspected of having, or be at risk of having a disease or a disorder described herein. In some embodiments, a disease or disorder may comprise an inflammatory bowel disorder. In some embodiments, an inflammatory bowel disorder may comprise an abnormal immune response. In some embodiments, an inflammatory bowel disorder may comprise but is not limited to one or more of the following: Crohn’s disease, ulcerative colitis, microscopic colitis, autoimmune enteropathy, celiac disease, chronic radiation enteritis, and / or diverticulitis. In some embodiments, a medical indication related to an inflammatory bowel disorder may comprise anydisease, disorder, or procedure (e.g., medical or surgical) that renders a subject wholly or partially immunocompromised or abnormally susceptible to infections. In some embodiments, a subject can have or be at an elevated risk for developing an infection. In some embodiments, a subject can have or be at an elevated risk for developing a cancer. In some embodiments, a subject can be receiving an immunosuppressant (e.g., chemotherapy, radiation, corticosteroids, transplant medications, or certain biologies), an anti-infective agent, antibiotic, antiviral agent, or antifungal agent. In some embodiments, a subject can be eligible as a recipient of transplantation or is an actual recipient of a transplanted organ or graft. In some embodiments, a subject can be an organ donor or preparing to be an organ donor. In some embodiments, a subject may comprise an animal organ donor for use in a xenotransplant or an animal being prepared for organ donation in a xenotransplant.

[0191] As used herein, “host” refers to an organism that harbors another organism or microbe. For example, a living thing e.g., a mammal such as a human being can be a host that harbors a microbe, the microbe being the non-host. As used herein, “host nucleic acids” and all derivative terms such as “host cell-free nucleic acids”, “host cell-free DNA”, etc. refer to nucleic acids derived from the host genome. In some embodiments, a host genome may comprise nucleic acids derived from a nucleus, a mitochondria, a cytoplasm, an exosome, cell-free nucleic acids derived from any of these, or any combination thereof.

[0192] Disclosed herein are methods and compositions for detecting target nucleic acids. In some embodiments, target nucleic acids may comprise host nucleic acids. In some embodiments, target nucleic acids may comprise non-host nucleic acids.Microbes

[0193] In some embodiments, non-host nucleic acids can be derived from a microbe. In some embodiments, target nucleic acids can be derived from a plurality of microbes. As used herein, a “microbe” can refer to a living microorganism or a non-living microscopic entity. In some embodiments, a living microorganism may comprise a bacterium, a protozoa, a fungus, an archaea, an algae, a parasite, or any other living microorganism. In some embodiments, a non-living microscopic entity may comprise a virus, a live virus, a replicating virus, or an attenuated virus.

[0194] In some embodiments, a microbe can be pathogenic to a subject (e.g., a pathogen), a commensal microbe of a subject, or a microbe present in a general environment. In some embodiments, a pathogen may comprise any pathogenic or virulent microbe. In some embodiments, a commensal microbe of a subject may comprise a microbe that inhabits any location in or on a subject without causing any symptom of a disease or disorder. In some embodiments, a microbe of a general environment may comprise a microbe at or near a samplecollection site or a microbe at or near a location of a subject. In some embodiments, a microbe of a general environment comprises a commensal microbe. In some embodiments, a commensal microbe of a subject may become a pathogen to the subject. In some embodiments, a commensal microbe of a first subject may be a pathogen to a second subject. In some embodiments, a microbe of a general environment of a subject may become a pathogen to a subject. In some embodiments, a microbe of a general environment of a first subject may be a pathogen to a second subject.

[0195] In some embodiments, a pathogen can cause an infection or disease comprising gastrointestinal infections (e.g., Escherichia coli, Salmonella spp., Clostridioides difficile), urinary infections (e.g., Escherichia coli , skin infections (e.g., Staphylococcus aureus, including MRSA), strep throat (or scarlet fever, rheumatic fever) (e.g., Streptococcus pyogenes), tuberculosis (e.g., Mycobacterium tuberculosis), gonorrhea (e.g., Neisseria gonorrhoeae), cholera (e.g., Vibrio cholerae), Lyme disease (e.g., Borrelia burgdorferi), ulcers or stomach cancer (e.g., Helicobacter pylori), syphilis (e.g., Treponema pallidum), anthrax (e.g., Bacillus anthracis), seasonal flu (e.g., Influenza viruses), acquired immunodeficiency syndrome (AIDS) (e.g., Human Immunodeficiency Virus (HIV)), liver infections (e.g., Hepatitis B and Hepatitis C viruses), cervical cancer (e.g., Human Papillomavirus (HPV)), respiratory infections (e.g., SARS-CoV-2), oral or genital herpes, (e.g., Herpes Simplex Virus (HSV-1 and HSV-2)), chickenpox or shingles (e.g., Varicella Zoster Virus), measles (e.g., Measles virus), neurological disorders (e.g., Rabies virus, Trypanosoma brucei), dengue fever (e.g., Dengue virus), Ebola disease (e.g., Ebola virus), candidiasis (e.g., Candida albicans), deep lung infections (e.g., Aspergillus spp., Pneumocystis jirovecii), histoplasmosis (e.g., Histoplasma capsulatum), meningitis (e.g., Cryptococcus neoformans), ringworm (e.g., Trichophyton spp.), malaria (e.g., Plasmodium spp.), intestinal infection (e.g., Ascaris lumbricoides), giardiasis (e.g., Giardia lamblia), amebiasis (e.g., Entamoeba histolytica), toxoplasmosis (e.g., Toxoplasma gondii), leishmaniasis (e.g., Leishmania spp.), schistosomiasis (e.g., Schistosoma spp.), strongyloidiasis (e.g., Strongyloides stercoralis), tapeworm, taeniasis, or cysticercosis (e.g., Taenia solium).

[0196] In some embodiments, commensal microbes can inhabit a gastrointestinal tract, a skin, a respiratory tract, aurogenital tract, or an oral cavity of a subject. In some embodiments, commensal microbes may comprise an endogenous virus (e.g., endogenous retroviruses (ERVs)) of a subject. In some embodiments, a commensal microbe may comprise Bacteroides fragilis, Lactobacillus acidophilus, a Bifidobacterium bifidum, an Escherichia coli (non-pathogenic strains), a Staphylococcus epidermidis, a Streptococcus salivarius, a Propionibacterium acnes, a Candida albicans (under normal conditions), a Enterococcus faecalis, a Clostridium difficile (non-toxigenic strains), a Rothia mucilaginosa, a Fusobacterium nucleatum, a Peptostreptococcus anaerobius, aPrevotella melaninogenica, or any combination thereof. In some embodiments, a commensal microbe may comprise a Lactobacillus spp., a Bacteroides spp., a Faecalibacterium prausnitzii, an Escherichia coli, a Clostridium spp., an Enterococcus spp., a Staphylococcus spp., a Candida spp., an Aspergillus spp., a Porcine Endogenous Retroviruses (PERVs), an Eimeria spp., a Bifidobacterium spp., a usobacterium spp., a Simian Immunodeficiency Virus (SIV), a Simian Retrovirus (SRV), a Entamoeba spp, or any combination thereof.Cell-free Nucleic acids

[0197] Disclosed herein are methods and compositions comprising nucleic acids. In some embodiments, a nucleic acid may comprise a cell-free nucleic acid (cfNA). In some embodiments, cfNAs may comprise any nucleic acids described herein that are not encapsulated by a cell. In some embodiments, cfNAs comprise naturally occurring cfNAs. In some embodiments, cfNAs may comprise fragments of nucleic acids that float freely outside of cells in any body fluid of a subject as described herein. In some embodiments, cfNAs may comprise plasma cfNAs, cerebrospinal fluid (CSF) cfNAs, saliva cfNAs, bronchoalveolar lavage (BAL) cfNAs, urine cfNAs, amniotic cfNAs, fetal cfNAs, or any combination thereof. In some cases, cfNAs comprise circulating cfNAs in a subject’s bloodstream. In some embodiments, the nucleic acids comprise circulating cfDNA, circulating cfRNA, cfDNA, cfRNA, circulating DNA, circulating RNA, or any combination thereof.

[0198] In some embodiments, cfNA can be alternatively referred to as free-circulating nucleic acids. In some embodiments, a cfNA can originate from cell death and other processes that release fragments of nucleic acids into a bloodstream. In some embodiments, a cfNA can be derived from any source of nucleic acids provided herein. In some embodiments, cfNA present in a raw biological sample can be isolated from genomic nucleic acid in the raw biological sample by processing the raw biological sample into an initial sample by removing intact cells. In some embodiments, removing intact cells may comprise centrifuging or filtering a raw biological sample to produce a cell-free fraction of a biological fluid comprising cfNA.

[0199] In some embodiments, a cfNA may comprise a host nucleic acid, a non-host nucleic acid, a target nucleic acid, or a combination thereof. In some embodiments, a cfNA can be derived from a host (host cell free nucleic acids or “hcfNA”) or a non-host. In some embodiments, a hcfNA can be derived from nuclear nucleic acids, mitochondria nucleic acids, exosomal nucleic acids, fetal nucleic acids, or any combination thereof. In some embodiments, a sample may comprise a host nucleic acid (e.g., a host cell-free nucleic acids). In some embodiments, a host may comprise any subject provided herein.

[0200] In some embodiments, a sample may comprise non-host nucleic acids. In some embodiments, non-host nucleic acids may comprise microbial nucleic acids. In some embodiments, microbial nucleic acids may comprise microbial cell-free nucleic acid (mcfNA). In some embodiments, the phrase “target nucleic acids” as used herein can refer to cfNA. In some embodiments, the phrase “target nucleic acids” as used herein can refer to a mcfNA. In some embodiments, an mcfNA can be derived from one or more species of microbe described herein. In some embodiments, a mcfNA can be derived from a prokaryotic or a eukaryotic microbe. In some embodiments, an mcfNA may comprise a bacterial cfNA, a fungal cfNA, a viral cfNA, a protozoan cfNA, an archaeal cfNA, an algal cfNA, or any combination thereof. In some embodiments, a sample may comprise a non-microbial nucleic acid (e.g., a non-microbial cell-free nucleic acid). In some embodiments, a sample may comprise mcfNAs from one or more species of microbes. In some embodiments, a sample may comprise mcfNAs from at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 species of microbes.

[0201] In some embodiments, a sample may comprise a mixture of nucleic acids. In some embodiments, a sample may comprise non-cell-free nucleic acids. In some embodiments, a sample may comprise cell-free nucleic acids. In some embodiments, a sample may comprise target nucleic acids (e.g., cfNAs) and can further additionally comprise any nucleic acids provided herein. In some embodiments, a sample can further comprise contaminant nucleic acids. In some embodiments, contaminant nucleic acids may comprise nucleic acids from a general environment (e.g., a sample collection site). In some embodiments, cell-free nucleic acids (cfNAs) may comprise a mixture of cfNAs. In some embodiments, a mixture of cfNAs may comprise cfNAs originated from one or more organisms. In some embodiments, a mixture of cfNAs may comprise microbial nucleic acids (e.g., mcfNAs) originated from one or more species of microbes described herein. In some embodiments, an mcfNA may comprise a bacterial-derived cfNA, a fungal-derived cfNA, a viral-derived cfNA, a protozoan-derived cfNA, an archaeal-derived cfNA, an algal- derived cfNA, or any combination thereof.

[0202] In some embodiments, a cfNA may comprise a double-stranded nucleic acid (dsNA), a single-stranded nucleic acid (ssNA), or a combination thereof. In some embodiments, a cfNA may comprise a cell-free DNA (cfDNA), a cell-free RNA (cfRNA), a cell-free DNA-RNA hybrid (cfDNA-RNA), a cell-free double-stranded DNA (cfdsDNA), a cell-free single-stranded DNA (cfssDNA), a cell-free double-stranded RNA (cfdsRNA), a cell-free single-stranded RNA(cfssRNA), or a combination thereof. In some embodiments, hcfNA may comprise host cell-free DNA (hcfDNA), host cell-free RNA (hcfRNA), host cell -free DNA-RNA hybrid (hcfDNA-RNA), or a combination thereof. In some embodiments, mcfNA may comprise microbial cell-free DNA (mcfDNA), microbial cell-free RNA (mcfRNA), microbial cell-free DNA-RNA hybrid (mcfDNA- RNA), or any combination thereof. In some embodiments, microbial cell-free DNA (mcfDNA) may comprise microbial cell-free double-stranded DNA (mcfdsDNA) or microbial cell-free single-stranded DNA (mcfssDNA). In some embodiments, microbial cell-free RNA (mcfRNA) may comprise microbial cell-free double-stranded RNA (mcfdsRNA) or microbial cell-free singlestranded RNA (mcfssRNA).Sizes of cfNAs

[0203] In some embodiments, a cfNA as disclosed herein or fragments thereof can be approximately less than about 10 bp, less than about 15 bp, less than about 20 bp, less than about 25 bp, less than about 30 bp, less than about 35 bp, less than about 40 bp, less than about 45 bp, less than about 50 bp, less than about 55 bp, less than about 60 bp, less than about 65 bp, less than about 70 bp, less than about 75 bp, less than about 80 bp, less than about 85 bp, less than about 90 bp, less than about 95 bp, less than about 100 bp, less than about 105 bp, less than about 110 bp, less than about 115 bp, less than about 120 bp, less than about 125 bp, less than about 130 bp, less than about 135 bp, less than about 140 bp, less than about 145 bp, less than about 150 bp, less than about 155 bp, less than about 160 bp, less than about 165 bp, less than about 170 bp, less than about 175 bp, less than about 180 bp, less than about 185 bp, less than about 190 bp, less than about 195 bp, or less than about 200 bp long.

[0204] In some embodiments, cfNAs provided herein or fragments thereof can be approximately about 10 bp, about 15 bp, about 20 bp, about 25 bp, about 30 bp, about 35 bp, about 40 bp, about 45 bp, about 50 bp, about 55 bp, about 60 bp, about 65 bp, about 70 bp, about 75 bp, about 80 bp, about 85 bp, about 90 bp, about 95 bp, about 100 bp, about 105 bp, about 110 bp, about 115 bp, about 120 bp, about 125 bp, about 130 bp, about 135 bp, about 140 bp, about 145 bp, about 150 bp, about 155 bp, about 160 bp, about 165 bp, about 170 bp, about 175 bp, about 180 bp, bout 185 bp, about 190 bp, about 195 bp, or about 200 bp long. In some embodiments, cfNAs provided herein or fragments thereof can be from about 10 bp to about 100 bp long. In some embodiments, the cfNAs provided herein or fragments thereof can be from about 30 bp to about 80 bp long. In some embodiments, the cfNAs provided herein or fragments thereof can be from about 40 bp to about 50 bp long.

[0205] In some embodiments, mcfNA can be present at higher concentrations relative to hcfNA at lengths that fall outside a nucleosomal interval. In some embodiments, mcfNA can be enrichedrelative to hcfNA by enriching for cfNA of less than 180bp, less than 170bp, less than 160bp, less than 150bp, less than 140bp, less than 130bp, less than 120bp, less than HObp, less than lOObp, less than 90bp, less than 80bp, less than 70bp, less than 60bp, less than 50bp, less than 40bp, less than 30bp, or less than 20bp. In some embodiments, enriching for mcfNA may comprise enriching for cfNA between 10-180 bp.

[0206] In some embodiments, a cfNA may comprise any nucleic acid described herein that is not encapsulated by a cell (e.g., a eukaryotic or microbial cell). In some embodiments, a cfNA can originate from any nucleic acids described herein. In some embodiments, a cfNA may comprise a plurality of chemical forms of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or DNA / RNA hybrid. In some embodiments, nucleic acids may comprise a plurality of structural forms of DNA, RNA, or DNA / RNA hybrid. In some embodiments, a cfNA may comprise linear nucleic acids or circular nucleic acids. In some embodiments, a cfNA may comprise single stranded nucleic acids (ssNA), double strand nucleic acids (dsNA) or hybrid nucleic acids. In some embodiments, nucleic acids can be from a genome of an organism or an organelle of a cell (e.g., an exosome or a mitochondria). In some embodiments, a cfNA may comprise a mitochondrial DNA, an intercellular signal nucleic acid, an exogenous nucleic acid, a DNA enzyme, a RNA enzyme, a food-derived nucleic acid, any metabolic form of nucleic acid-based therapeutic, or any combination thereof. In some embodiments, a cfNA can be derived from a member selected from the group consisting of genomic DNA, cDNA, mRNA, cRNA, tRNA, ribosomal RNA, miRNA, siRNA, nuclear DNA, nuclear RNA, mitochondrial DNA, mitochondrial RNA, exosomal DNA, exosomal RNA, fetal DNA, fetal RNA, plasmids, vectors, and any combination thereof.

[0207] In some embodiments, nucleic acids may comprise a mixture of nucleic acids from various sources. In some embodiments, nucleic acids can be derived from a plurality of biological fluids. In some embodiments, nucleic acids can be from a plurality of organisms. In some embodiments, nucleic acids can be from a subject described herein. In some embodiments, nucleic acids can be from one or more species of microbes described herein. In some embodiments, nucleic acids may comprise environmental nucleic acids. In some embodiments, environmental nucleic acids may comprise any nucleic acid at or near a sample collection site, or any nucleic acid introduced by personnel, equipment or a reagent used in collecting and / or processing a sample from a subject.Assay Performance

[0208] In some embodiments, performance of a machine-learning classifier as disclosed herein ...

Claims

CLAIMSWhat is claimed is:

1. A method of detecting a subtype of inflammatory bowel disease (IBD) in a subject, the method comprising:(a) providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises subject cell-free nucleic acids (subject cfNA), microbial cell-free nucleic acids (mcfNA), or a mixture thereof;(b) performing a sequencing assay on the cfNA to obtain sequence data;(c) applying a classifier to the sequence data, wherein the classifier can detect at least one subtype of IBD based on an mcfNA signature, a subject cfNA signature, or a combination thereof; and(d) determining that the subject has a subtype of inflammatory bowel disorder based at least in part on the applying of the classifier to the sequence data.

2. The method of claim 1, wherein the classifier can detect ulcerative colitis (UC) or Crohn’s disease (CD) in the subject.

3. The method of claim 1, wherein the classifier can distinguish between UC and CD in the subject.

4. The method of claim 2 or 3, wherein the classifier detects UC, detects CD, or distinguishes between UC and CD at an AUC of greater than 0.7.

5. The method of any one of claims 1-4, wherein, prior to (b), the subject is determined to have IBD with an unknown subtype.

6. The method of any one of claims 1-4, wherein the subject has previously had an endoscopy procedure.

7. The method of claim 6, wherein the endoscopy procedure indicated that the subject had indeterminate colitis.

8. The method of any one of the preceding claims, wherein the classifier can detect at least one subtype of IBD based on an mcfNA signature and wherein the sequence data comprises data from mcfNA in the sample.

9. The method of any one of the preceding claims, wherein the classifier can detect at least one subtype of IBD based on an mcfNA signature and on a subject cfNA signature and wherein the sequence data comprises data from mcfNA in the sample and the subject cfNA in the sample.

10. A method of detecting a severity of inflammatory bowel disease (IBD) in a subject, the method comprising:(a) providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprise subject cell-free nucleic acids (subject cfNA), microbial cell-free nucleic acids (mcfNA), or a mixture thereof;(b) performing a sequencing assay on the cfNA to obtain sequence data;(c) applying a classifier to the sequence data, wherein the classifier can detect any of the following categories of severity: mild disease, moderate disease, severe disease, remission, or combination thereof; and(d) categorizing severity of disease in the subject based at least in part on the applying of the classifier to the sequence data.

11. The method of claim 10, wherein the categorizing in (d) comprises determining that the subject is in remission.

12. The method of claim 10, wherein the categorizing in (d) comprises determining that the subject has mild, moderate, or severe IBD.

13. The method of any one of claims 10-12, wherein the categorizing in (d) further comprises detecting a level of severity of a subtype of IBD.

14. The method of claim 13, wherein the subtype of IBD is ulcerative colitis (UC) or Crohn’s disease (CD).

15. A method of preparing a cell-free nucleic acids (cfNA) fraction from a subject with an inflammatory bowel disease (IBD) of unknown subtype comprising:(a) providing an initial sample from the subject with the IBD of unknown subtype, the initial sample comprising cfNA comprising subject cell-free nucleic acids (subject cfNA), microbial cell-free nucleic acids (mcfNA), or a mixture thereof and wherein the cfNA comprises double-stranded cfNA, single-stranded cfNA, degraded double-stranded cfNA (degraded dscfNA) and degraded single-stranded cfNA (degraded sscfNA);(b) denaturing the double-stranded cfNA and degraded dscfNA into single-stranded fragments such that the cfNA comprises: (i) the single-stranded cfNA and the degraded sscfNA originally in the initial sample; and (ii) single-stranded cfNA fragments and degraded sscfNA fragments produced by the denaturing of the double-stranded cfNA;(c) preparing a cfNA library comprising cfNA produced in (b); and(d) analyzing a genetic locus within the single-stranded cfNA fragments, wherein the genetic locus is located within the mcfNA, the subject cfNA, or both.

16. The method of claim 15, wherein the cfNA comprise cfNA fragments at least 20 bases in length.

17. The method of any of one of the preceding claims, wherein the cfNA comprises cfNA fragments less than 200 bases in length.

18. The method of any of one of the preceding claims, wherein the cfNA comprises cfNA fragments less than 100 bases in length.

19. The method of any one of the preceding claims, wherein the genetic locus is located within the mcfNA.

20. The method of any one of the preceding claims, wherein the genetic locus is located within single-stranded cfNA or degraded sscfNA in the initial sample.

21. The method of any one of the preceding claims, wherein the genetic locus is located within double-stranded cfNA or degraded dscfNA in the initial sample.

22. The method of any one of the preceding claims, wherein the preparing a cfNA library comprises attaching 5’ adapters, 3’ adapters, or both 5’ and 3’ adapters to the cfNA.

23. The method of claim 22, wherein the attaching 5’ adapters, 3’ adapters, or both 5’ and 3’ adapters to the cfNA occurs in the initial sample wherein the initial sample has not been subjected to an extraction assay.

24. A method of preparing a cell-free nucleic acids fraction from a subject with an inflammatory bowel disease (IBD) comprising:(a) providing a sample from the subject with the IBD, the sample comprising: cell-free nucleic acids (cfNA), wherein the cfNA comprise subject cell-free nucleic acids (subject cfNA), microbial cell-free nucleic acids (mcfNA), or a mixture thereof.(b) physically enriching the sample for subject cfNA, mcfNA fragments, or both, that are less than a cutoff value between 70-200 bases to produce a size-enriched fraction of cfNA; and(c) analyzing a genetic locus in the size-enriched fraction of cfNA, wherein the genetic locus is located within the mcfNA, the subject cfNA, or both.

25. The method of any one of the preceding claims, wherein the genetic locus comprises a plurality of genetic loci that constitute a signature that distinguishes between ulcerative colitis (UC) and Crohn’s disease (CD).

26. The method of any one of claims 24-25, wherein the cutoff value is less than about 90 bases.

27. The method of any one of the preceding claims, further comprising physically enriching the sample for subject cfNA and mcfNA greater than about 10 bases in length.

28. The method of any one of the preceding claims, wherein the genetic locus analyzed in the size-enriched fraction of cfNA is located within the mcfNA.

29. The method of any one of the preceding claims, wherein the physically enriching comprises directly physically enriching the sample or indirectly physically enriching the sample.

30. The method of claim 29, wherein the directly physically enriching comprises subjecting the cfNA to a size selection device.

31. The method of claim 30, wherein the size selection device comprises beads or a gel electrophoresis device.

32. The method of claim 29, comprising the indirectly physically enriching, wherein the indirectly physically enriching results from a process that does not involve use of sharp cutoff values for size selection.

33. The method of any one of the preceding claims, further comprising screening the subject for IBD prior to, simultaneously, or following the providing the sample from the subject in(a).

34. The method of any one of the preceding claims, further comprising performing an endoscopic procedure on the subject that identifies the subject as having indeterminate colitis or obtaining results from an endoscopic procedure performed on the subject, wherein the endoscopic procedure indicated the subject has indeterminate colitis.

35. The method of claim 34, wherein the endoscopic procedure is performed prior to, simultaneously, or following the providing the sample from the subject in (a).

36. The method of any one of the preceding claims, wherein the physically enriching comprises enriching the sample for degraded cfNA.

37. A method of treating a subject diagnosed as having a subtype of Inflammatory Bowel Disease (IBD), the method comprising: treating the subject for the subtype of IBD by administering a medicament for the subtype of IBD to the subject, wherein the diagnosis is based at least in part on a method comprising:(a) providing a sample from the subject, wherein the subject has an unknown subtype of inflammatory bowel disease (IBD), the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises a mixture of subject cell-free nucleic acids (subject cfNA) and microbial cell-free nucleic acids (mcfNA);(b) performing a sequencing assay on the cfNA to obtain sequence data;(c) applying a classifier to the sequence data, wherein the classifier can detect at least one subtype of IBD based on a mcfNA signature, a subject cfNA signature, or a combination thereof; and(d) determining that the subject has a subtype of inflammatory bowel disorder based at least in part on the applying of the classifier to the sequence data.

38. A method of treating a subject diagnosed as having a subtype of Inflammatory Bowel Disease (IBD) categorized as severe, moderate, mild, or in remission, the method comprising: treating the subject for the subtype of IBD by administering a medicament for the subtype of IBD to the subject at a dose consistent with the severity of IBD, wherein the diagnosis is based at least in part on a method comprising:(a) providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises a mixture of subject cell-free nucleic acids (subject cfNA) and microbial cell-free nucleic acids (mcfNA);(b) performing a sequencing assay on the cfNA to obtain sequence data;(c) applying a classifier to the sequence data, wherein the classifier can categorize severity of a subtype of IBD based on a mcfNA signature, a subject cfNA signature, or a combination thereof; and(d) categorizing the severity of the subtype of IBD in the subject as severe, moderate, mild, or in remission, based at least in part on the applying of the classifier to the sequence data.

39. A method of treating and monitoring a subject diagnosed as having an Inflammatory Bowel Disease (IBD) subtype in remission, the method comprising:(a) treating the subject for the IBD subtype in remission by administering a first medicament to the subject at an initial maintenance dose;(b) between 2 weeks to 6 months after (a), providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises a mixture of subject cell-free nucleic acids (subject cfNA) and microbial cell-free nucleic acids (mcfNA);(c) performing a sequencing assay on the mixture of mcfNA and subj ect cfNA to obtain sequence data;(d) applying a classifier to the sequence data, wherein the classifier can categorize a subtype of IBD as being severe, moderate, mild, or in remission, based on a mcfNA signature, a subject cfNA signature, or a combination thereof;(e) categorizing the subtype of IBD as severe, moderate, mild or in remission, based at least in part on the applying of the classifier to the sequence data; and(f) if the subtype of IBD is categorized as in remission, continuing to treat the subject with the first medicament at the initial maintenance dose, reducing the dose of the first medicament, or discontinuing use of the first medicament; and if the subtype of IBD is categorized as mild, moderate or severe, treating the subject by:(i) increasing the dose of the first medicament to a dose higher than the first initial maintenance dose;(ii) administering a second medicament to the subject in addition to, or in place of, the first medicament;(iii) performing an endoscopic procedure on the subj ect in order to detect the severity of the subtype of IBD and identify the location of the subtype of IBD; or(iv) performing a surgery on the subject in order to remove a portion of the digestive tract of the subject if the endoscopic procedure confirms that the subject is suffering from a moderate or severe subtype of IBD.

40. A method of treating and monitoring a subj ect diagnosed as having an Inflammatory Bowel Disease (IBD) subtype, the method comprising:(a) treating the subject for the IBD subtype by administering a first medicament to the subject at an initial induction dose;(b) about 2 to 6 weeks after (a), providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises a mixture of subject cell-free nucleic acids (subject cfNA) and microbial cell-free nucleic acids (mcfNA);(c) performing a sequencing assay on the mixture of mcfNA and subj ect cfNA to obtain sequence data;(d) applying a classifier to the sequence data, wherein the classifier can categorize a subtype of IBD as being severe, moderate, mild, or in remission, based on a mcfNA signature, a subject cfNA signature, or a combination thereof;(e) categorizing the subtype of IBD as severe, moderate, mild or in remission, based at least in part on the applying of the classifier to the sequence data; and(f) if the subtype of IBD is categorized as in remission, continuing to treat the subject with the first medicament at the initial induction dose, reducing the dose of the first medicament, or discontinuing use of the first medicament; and(g) if the subtype of IBD is categorized as mild, moderate or severe, and indicates the subject is not responding to the first medicament, treating the subject by:(i) increasing the dose of the first medicament to a dose higher than the first initial induction dose;(ii) administering a second medicament to the subject in addition to, or in place of, the first medicament;(iii) performing an endoscopic procedure on the subj ect in order to detect the severity of the subtype of IBD and identify the location of the subtype of IBD; or(iv) performing a surgery on the subject in order to remove a portion of the digestive tract of the subject if the endoscopic procedure confirms that the subject is suffering from a moderate or severe subtype of IBD.

41. A method of treating and monitoring a subject wherein the subject has received a surgical intervention for an Inflammatory Bowel Disease (IBD) subtype, the method comprising:(a) at least 2-6 weeks following the surgical intervention, providing a sample from the subject, the sample comprising cell-free nucleic acids (cfNA), wherein the cfNA comprises a mixture of subject cell-free nucleic acids (subject cfNA) and microbial cell-free nucleic acids (mcfNA);(b) performing a sequencing assay on the mixture of mcfNA and subj ect cfNA to obtain sequence data;(c) applying a classifier to the sequence data, wherein the classifier can categorize a subtype of IBD as being severe, moderate, mild, or in remission, based on a mcfNA signature, a subject cfNA signature, or a combination thereof;(d) categorizing the subtype of IBD as severe, moderate, mild or in remission, based at least in part on the applying of the classifier to the sequence data; and(e) if the subtype of IBD is categorized as in remission, administer, or continue to administer, a maintenance therapy; and if the subtype of IBD is categorized as mild, moderate or severe, treating the subject by:(i) adjusting the subj ect’ s treatment regimen by adding or subtracting a medication or changing a dose of a medication;(ii) performing an endoscopic procedure on the subj ect in order to detect the severity or location of the subtype of IBD and identify the location of the subtype of IBD; or(iii) performing another surgery on the subject in order to remove a portion of the digestive tract of the subject if the endoscopic procedure confirms that the subject is suffering from a moderate or severe subtype of IBD.

42. The method of any one of the preceding claims, wherein an endoscopic procedure performed prior to (a) has indicated the subject has indeterminate colitis.

43. The method of any claim 42, wherein the IBD is considered to be indeterminate because of inaccessible regions of the bowel or because of indeterminate disease manifestation.

44. The method of claim 42 or 43, wherein the indeterminate disease manifestation is due to a finding of continuous inflammatory patches that could be consistent with CD or UC.

45. The method of any one of the preceding claims, wherein the classifier can detect ulcerative colitis (UC) or Crohn’s disease (CD).

46. The method of any one of the preceding claims, wherein the classifier can distinguish between UC and CD.

47. The method of any one of the preceding claims, wherein if the subject is determined to be in remission, further comprising administering a maintenance treatment to the subject.

48. The method of claim 47, wherein the maintenance therapy comprises an anti-inflammatory drug or cortico-steroid.

49. The method of any one of the preceding claims, wherein if the subject is determined to have mild, moderate, or severe disease, administering a drug for mild, moderate, or severe disease.

50. The method of any one of the preceding claims, wherein if a subject is determined to have a mild, moderate, or severe subtype of IBD, and the subject is receiving a drug regimen, further comprising adjusting or changing the drug regimen.

51. The method of any one of the preceding claims, further comprising, if the subject is determined to have mild, moderate, or severe disease, performing an endoscopy on the subject in order to identify regions of inflammation.

52. The method of any one of the preceding claims, wherein if the subject is determined to have mild, moderate, or severe disease, performing surgery on the patient to remove all of, or a portion of, the anus, rectum, large intestine, small intestine, digestive tract, or any combination thereof.

53. The method of any one of the preceding claims, wherein the screening of the subject comprises detection of a lesion, ulceration, inflammation, bleeding pattern, or disease location in the gastrointestinal tract.

54. The method of claim any one of the preceding claims, wherein the subject has an indeterminate endoscopic biopsy prior to the providing the sample in (a).

55. The method of claim 54, wherein the subject has had an indeterminate biopsy that detected continuous inflammatory regions or lesions along a section of the gastrointestinal tract.

56. The method of claim 54 or 55, wherein the subject has had an endoscopic procedure of the gastrointestinal tract that results in a finding of IBD, UC, CD, or combination thereof.

57. The method of claim 56, wherein the method is performed in order to confirm the finding of IBD, UC, CD, or combination thereof.

58. The method of any one of the preceding claims, further comprising performing an endoscopic procedure on the gastrointestinal tract of the subject if UC, CD, mild disease, moderate disease, or severe disease is detected by the method.

59. A method of guiding an endoscopic procedure comprising:(a) collecting a sample from a patient with an inflammatory bowel disease (IBD) of unknown subtype, wherein:(i) the sample comprises cell-free nucleic acids (cfNA) comprising human cell-free nucleic acids (human cfNA), microbial cell-free nucleic acids (mcfNA), or a mixture thereof;(ii) the patient is planning to undergo an endoscopy procedure; and(iii) the sites to be biopsied by the endoscopy procedure have not yet been determined;(b) performing a sequencing assay on the cfNA to obtain sequence data;(c) applying a classifier to the sequence data, wherein the classifier can distinguish between at least two types of inflammatory bowel disorder (IBD) based on a mcfNA signature, a subject cfNA signature, or a combination thereof; and(d) determining that the subject has a first type of IBD based at least in part on the applying of the classifier to the sequence data, wherein:(i) the first type of IBD is associated with inflammatory regions along the entirety of the digestive tract and,(ii) the second type of IBD is associated with inflammatory regions localized to the large intestine, the rectum, or both the large intestine and the rectum; and wherein if the first type of IBD is detected, an endoscopic procedure is performed that targets multiple locations along the entirety of the digestive tract; and if the second type ofIBD is detected, an endoscopic procedure is performed that targets a region limited to the large intestine and the rectum.

60. The method of any claim 59, wherein the first type of IBD is Crohn’s disease (CD).

61. The method of claim 59 or 60, wherein the second type of IBD is ulcerative colitis (UC).

62. The method of any one of claims 59-61, wherein the at least two types of IBD comprise at least two of mild IBD, moderate IBD, severe IBD, or IBD in remission.

63. The method of any one of the preceding claims, further comprising screening the subject for IBD.

64. The method of any one of the preceding claims, wherein the screening comprises a physical examination, blood test, stool test, imaging study, reported symptoms, medications, personal medical history, family medical history, or any combination thereof.

65. The method of any one of the preceding claims, wherein the screening comprises a clinical evaluation based on one or more features selected from the group consisting of abdominal pain, rectal bleeding, weight loss, fatigue, personal medical history, family medical history, lifestyle, or any combination thereof.

66. The method of any one of the preceding claims, wherein the screening is inconclusive for IBD, subtype of IBD, or severity of subtype of IBD.

67. The method of any one of claims 1-66, further comprising physically enriching the sample for human and microbial cell-free nucleic acid fragments that are less than a cutoff value between 70-200 bases.

68. The method of any one of claims 1-67, wherein the physically enriching comprises producing a size-enriched fraction of the cfNA by:(a) binding the cfNA to a solid support capable of separating the cfNA based on size and eluting the cfNA from the solid support to obtain size-selected cfNA;(b) subjecting the cfNA to a size-selection electrophoresis; or(c) a combination of (a) and (b).

69. The method of any one of the preceding claims, wherein the method further comprises analyzing a genetic locus in the size-enriched fraction of cfNA.

70. The method of claim 69, wherein the analyzing the genetic locus in the size-enriched fraction of cfNA comprises sequencing the size-enriched fraction of cfNA to obtain sequence reads.

71. The method of any claim 69 or 70, wherein the analyzing the genetic locus comprises determining a ratio of a number of sequence reads covering the genetic locus to the number of reads covering a flanking region.

72. The method of claim 71, wherein the number of sequence reads covering the first genomic region comprises the number of sequence reads within 500 bp of the genetic locus, and wherein the number of sequence reads covering the flanking region comprises a number of sequence reads located more than 500bp from the genetic locus but within 2000 bp in either a 5’ or 3’ direction from the genetic locus.

73. The method of claim 71 or 72, wherein the ratio comprises a natural log of the number of sequence reads covering the first genomic region divided by the number of sequence reads covering the flanking region.

74. The method of any one of claims 70-73, wherein the ratio comprises a peak-to-flank ratio or a trough-to-flank ratio of sequence reads.

75. The method of any one of claims 70-74, further comprising determining that a gene is differentially enriched when the value of the ratio for the gene is 0.3 or greater.

76. The method of any one of claims 1-75, wherein the sample comprises a biological fluid.

77. The method of any one of the preceding claims, wherein the method further comprises analyzing a genetic locus in the mcfNA or the subject cfNA, or a combination thereof.

78. The method of any one of the preceding claims, further comprising analyzing a genetic locus within a human genome.

79. The method of any one of claims 1-78, wherein the genetic locus is within microbial cell- free DNA derived from a Propionibactierum, a Lactococcus, a Haemophilus, an Escherichia, a Rothia, a Malassezia, a Streptococcus, a Rothia, an Actinomyces, a Klebsiella, a Dermacoccus, an Acinetobacter, Lactobacillus, or any combination thereof.

80. The method of any one of claims 1-79, wherein the genetic locus is within microbial cell- free DNA derived from Acinetobacter, Staphylococcus, Blautia, Anoxybacillus, Paracoccus, or any combination thereof.

81. The method of any one of claims 1-80, wherein the analyzing comprises performing high throughput sequencing on the sample.

82. The method of claim 81, wherein the biological fluid is a non-fecal biological fluid.

83. The method of any one of claims 1-82, wherein the sample comprises blood, serum, plasma, cerebrospinal fluid, fluid from lavage, fluid from bronchoalveolar lavage, synovial fluid, or urine.

84. The method of any one of claims 1-83, wherein the sample is a plasma sample.

85. The method of any one of claims 1-84, wherein the sample comprises cfNA derived from or purified from a biological fluid.

86. The method of any one of claims 1-85, wherein the subject with an inflammatory bowel disorder has symptoms consistent with both ulcerative colitis and Crohn’s Disease.

87. The method of claim 86, wherein the symptoms comprise: long-term inflammation of the digestive tract, digestive discomfort, stomach cramps and pain, diarrhea, constipation, urgent need to have a bowel movement, feeling as though a bowel movement was incomplete, rectal bleeding, loss of appetite, weight loss, fatigue, night sweats, irregular periods, or any combination thereof.

88. The method of any one of claims 1-87, wherein the subject is human.

89. The method of any one of claims 1-88, further comprising administering a medicament to the subject.

90. The method of any one of claims 1-89, further comprising distinguishing between a first, a second and a third type of inflammatory bowel disease or disorder.

91. The method of any one of the preceding claims, wherein the analyzing comprises analyzing data generated from sequence reads obtained from both the human and mcfNA.

92. The method of any one of the preceding claims, wherein the first type of inflammatory bowel disease or disorder comprises a severe inflammatory bowel disease or disorder and the second type of inflammatory bowel disease or disorder comprises a moderate inflammatory bowel disease.

93. The method of any one of the preceding claims, further comprising distinguishing between a first, a second and a third type of inflammatory bowel disease or disorder.

94. The method of claim 93, wherein the third type of inflammatory bowel disease or disorder comprises a mild inflammatory bowel disease or disorder.

95. The method of any one of the preceding claims, wherein the method further comprises determining that the inflammatory bowel disorder comprises Crohn’s disease.

96. The method of any one of the preceding claims, wherein the method further comprises determining that the inflammatory bowel disorder comprises Ulcerative colitis.

97. The method of any one of the preceding claims, wherein the analyzing the sequence reads comprises use of machine learning.

98. The method of any one of the preceding claims, wherein the analyzing the sequence reads comprises applying one or more classifiers to sequence data.

99. The method of claim 98, wherein the one or more classifiers are assessed using a receiver operating characteristics curve (ROC).

100. The method of any one of the preceding claims, further comprising determining a diversity of overall detected microbes from the microbial cell-free DNA, wherein the subject isdetermined to have an active disease when the sample from the subject has a higher alpha diversity of overall detected microbes relative to an otherwise comparable sample with a lower alpha diversity of overall detected microbes.

101. The method of any one of the preceding claims, further comprising determining the disease is severe, and wherein the determining comprises detecting a higher alpha diversity of overall detected microbes in the sample from the subject relative to an otherwise comparable sample with a lower alpha diversity of overall detected microbes.

102. The method of any one of claims 1-101, further comprising determining the disease comprises ulcerative colitis, wherein the determining comprises analyzing the sequence reads to detect in the sample a presence of cell-free DNA derived from a Propionibactierum, a Lactococcus, Haemophilus, an Escherichia, Rothia, aMalassezia, a Streptococcus, Rothia, a Malassezia, an Actinomyces, a Klebsiella, a Dermacoccus, an Acinetobacter, a Lactobacillus, or any combination thereof .

103. The method of any one of claims 1-102, further comprising determining the disease comprises ulcerative colitis, wherein the determining comprises analyzing the sequence reads to detect in the sample a presence of cell-free DNA derived from an Afipia, a Bifidobacterium, a Brochothrix, a Companilactobacillus, a Coprobacillus, an Escherichia, a Leptospira, a Methylobacterium, a Pantoea, a Parasutterella, a Pichia, a Proteus, a Sphingobacterium, an Achromobacter, an Acinetobacter, an Actinomyces, an Aeribacillus, an Alishewanella, an Alistipes, an Alphacoronavirus, an Alphainfluenzavirus, an Anoxybacillus, an Aureobasidium, a Bacillus, a Betacoronavirus, a Blautia, a Burkholderia, a Caldibacillus, a Caldicellulosiruptor, a Campylobacter, aCapnocytophaga, a Chryseobacterium, a Citrobacter, a Clostridia UnClass UnClass UnClass, a Clostridium, a Collinsella, a Coprococcus, a Cupriavidus, a Cyberlindnera, a Delftia, a Dependoparvovirus, a Dialister, a Duffyella, an Emesvirus, an Enhydrobacter, an Enter obacter, an Eubacteriales Family XIII. Incertae Sedis UnClass, an Eubacteriales UnClass UnClass, an Eubacterium, a Finegoldia, a Francisella, a Geobacillus, an Inovirus, an Intestinibacter, a Kingella, a Klebsiella, a Kocuria, a Lachnoanaerobaculum, a Lachnoclostridium, a Lentivirus, a Leuconostoc, a Mediterraneibacter, a Megasphaera, a Melampsora, a Mesorhizobium, a Methanococcus, a Methanosarcina, a Methanothrix, a Methylorubrum, a Moraxella, a Mycobacterium, a Mycolicibacterium, a Nesterenkonia, an Orthopoxvirus, a Paenibacillus, a Paenirhodobacter, a Paraburkholderia, a Paracoccus, a Pelomonas, a Prevotella, a Pseudomonas, a Ralstonia, a Rhodococcus, a Rothia, a Ruminococcus, a Saccharomyces,a Schaalia, a Selenomonas, a Sphingobium, a Sphingomonas, a Staphylococcus, a Stenotrophomonas, a Stomatobaculum, a Stutzerimonas, a Sulfurihydrogenibium, a Sutterella, a Tepidimonas, a Tepidiphilus, a Teseptimavirus, a Thermicanus, a Thermoanaerobacterium, a Thomasclavelia, a Trichuris, a Tyzzerella, a Variovorax, a Veillonella, a Weizmannia, a Williamsia, an Enterococcus, an Alicyclobacillus, a Bacteria UnClass UnClass UnClass UnClass UnClass, a Bradyrhizobium, a Brucella, a Curvibacter, a Dermacoccus, an Elaeophora, a Faecalibacterium, a Flavonifr actor, a Halomonas, a Lachnospira, a Lacticaseibacillus, a Lambdavirus, a Liquor ilactobacillus, a Lymphocryptovirus, a Novosphingobium, a Rhizopus, a Rhodopseudomonas, a Roseburia, a Schizosaccharomyces, a Streptomyces, a Tequatrovirus, a Vedamuthuvirus, a Fervidobacterium, a Microbacterium, a Retroviridae UnClass, a Neurospora, a Pseudacidovorax, or any combination thereof.

104. The method of any one of claims 1-103, further comprising determining the disease comprises Crohn’s disease, wherein the determining comprises analyzing the sequence reads to detect in the sample a presence of cell-free DNA derived from Propionibactierum, Lactococcus, Haemophilus, Escherichia, Rothia, Malassezia, Streptococcus, Actinomyces, Klebsiella, Dermacoccus, Acinetobacter, Lactobacillus, or any combination thereof.

105. The method of any one of claims 1-104, further comprising determining the disease is Crohn’s disease, wherein the determining comprises analyzing the sequence reads to detect in the sample a presence of cell-free DNA derived from an Afipia, a Bifidobacterium, a Brochothrix, a Companilactobacillus, a Coprobacillus, an Escherichia, a Leptospira, a Methylobacterium, a Pantoea, a Parasutterella, a Pichia, a Proteus, a Sphingobacterium, an Achromobacter, an Acinetobacter, an Actinomyces, an Aeribacillus, an Alishewanella, an Alistipes, an Alphacoronavirus, an Alphainfluenzavirus, an Anoxybacillus, an Aureobasidium, a Bacillus, a Betacoronavirus, aBlautia, a Burkholderia, a Caldibacillus, a Caldicellulosiruptor, a Campylobacter, a Capnocytophaga, a Chryseobacterium, a Citrobacter, a Clostridia UnClass UnClass UnClass, a Clostridium, a Collinsella, a Coprococcus, a Cupriavidus, a Cyberlindnera, a Delftia, a Dependoparvovirus, a Dialister, aDuffyella, an Emesvirus, an Enhydrobacter, an Enter obacter, an Eubacteriales Family XIII. Incertae Sedis UnClass, an Eubacteriales UnClass UnClass, an Eubacterium, a Finegoldia, a Francisella, a Geobacillus, an Inovirus, an Intestinibacter, a Kingella, a Klebsiella, a Kocuria, a Lachnoanaerobaculum, a Lachnoclostridium, a Lentivirus, a Leuconostoc, a Mediterraneibacter, a Megasphaera, a Melampsora, a Mesorhizobium, a Methanococcus, a Methanosarcina, a Methanothrix, a Methylorubrum,a Moraxella, a Mycobacterium, a Mycolicibacterium, a Nesterenkonia, an Orthopoxvirus, a Paenibacillus, a Paenirhodobacter, a Paraburkholderia, a Paracoccus, a Pelomonas, a Prevotella, a Pseudomonas, a Ralstonia, a Rhodococcus, a Rothia, a Ruminococcus, a Saccharomyces, a Schaalia, a Selenomonas, a Sphingobium, a Sphingomonas, a Staphylococcus, a Stenotrophomonas, a Stomatobaculum, a Stutzerimonas, a Sulfurihydrogenibium, a Sutterella, a Tepidimonas, a Tepidiphilus, a Teseptimavirus, a Thermicanus, a Thermoanaerobacterium, a Thomasclavelia, a Trichuris, a Tyzzerella, a Variovorax, a Veillonella, a Weizmannia, a Williamsia, an Enterococcus, an Alicyclobacillus, a Bacteria UnClass UnClass UnClass UnClass UnClass, a Bradyrhizobium, a Brucella, a Curvibacter, a Dermacoccus, an Elaeophora, a Faecalibacterium, a Flavonifr actor, a Halomonas, a Lachnospira, a Lacticaseibacillus, a Lambdavirus, a Liquorilactobacillus, a Lymphocryptovirus, a Novosphingobium, a Rhizopus, a Rhodopseudomonas, a Roseburia, a Schizosaccharomyces, a Streptomyces, a Tequatrovirus, a Vedamuthuvirus, a Fervidobacterium, a Microbacterium, a Retroviridae UnClass, a Neurospora, a Pseudacidovorax, or any combination thereof.

106. The method of any one of claims 1-105, further comprising determining the disease comprises mild, moderate, or severe ulcerative colitis, wherein the determining comprises analyzing the sequence reads to detect an elevated or decreased level of cell-free DNA in the sample derived from Acinetobacter, Staphylococcus, Blautia, Anoxybacillus, Paracoccus, or any combination thereof, relative to an otherwise comparable sample from a subject that is asymptomatic or in remission for ulcerative colitis.

107. The method of any one of claims 1-106, further comprising determining the disease comprises mild, moderate, or severe ulcerative colitis, wherein the determining comprises analyzing the sequence reads to detect an elevated or decreased level of cell-free DNA in the sample derived from an Uroviricota, a Chromadorea, a Clostridia, a Coriobacteriia, a Sordariomycetes, a Eubacteriales, a Propionibacteriales, a Sordariales, an Alicyclobacillaceae, a Bacteroidaceae, a Burkholder iales UnClass, aCaudoviricetes UnClass UnClass, a Clostridiaceae, an Eubacteriales UnClass, a Lachnospiraceae, a Micrococcaceae, an Onchocercidae, an Oscillospiraceae, a Phyllobacteriaceae, a Propionibacteriaceae, a Sordariaceae, a Streptococcaceae, a Sutterellaceae, an Alicyclobacillus, a Bacillus, a Blautia, a Caldibacillus, a Ceduovirus, a Clostridium, a Collinsella, a Coprococcus, a Delftia, a Dorea, an Enter ocloster, an Eubacteriales UnClass UnClass, a Faecalibacterium, a Flavonifr actor, a Kocuria, a Lachnospira, a Lachnospiraceae UnClass, a Lambdavirus, a Mediterraneibacter, aMicrococcus, a Moineauvirus, a Neurospora, a Novosphingobium, a Roseburia, a Ruminococcus, a Skunavirus, a Sphingobium, a Tepidimonas, a Tyzzerella, an Acinetobacter or any combination thereof, relative to an otherwise comparable sample from a subject that is asymptomatic or in remission for ulcerative colitis.

108. The method of any one of claims 1-107, further comprising determining the disease comprises mild, moderate, or severe Crohn’s disease, wherein the determining comprises analyzing the sequence reads to detect an elevated presence of cell-free DNA in the sample derived from Malassezia, Acinetobacter, Streptococcus, Lactobacillus, Lactobacillus, or any combination thereof, relative to an otherwise comparable sample from a subject that is asymptomatic or in remission for Crohn’s disease.

109. The method of any one of claims 1-108, further comprising determining the disease comprises mild, moderate, or severe Crohn’s disease, wherein the determining comprises analyzing the sequence reads to detect an elevated presence of cell-free DNA in the sample derived from Malassezia restricta, Acinetobacter baumannii, Streptococcus sanguinis. Lactobacillus plantarum, Lactobacillus crispatus, or any combination thereof, relative to an otherwise comparable sample from a subject that is asymptomatic or in remission for Crohn’s disease.

110. The method of any one of claims 1-109, further comprising determining that the subject has a disease based at least in part on the analyzing the genetic locus.

111. The method of claim 110, wherein the determining that the subject has a disease based on the biomarkers comprises a sensitivity of AUC >0.95.

112. The method of any one of claims 1-111, wherein the sequencing comprises sequencing 100 million to 400 million paired-end reads per sample.

113. The method of claim 112, wherein the sequencing comprises sequencing 300 million to 400 million paired-end reads per sample.

114. The method of any one of claims 1-113, wherein the sequencing comprises from 5X to 10X average coverage per base pair per sample.

115. The method of any one of claims 1-114, wherein the sequencing further comprises enriching for cell-free nucleic acids of less than 170 base pairs in length.

116. The method of any one of claims 1-115, wherein the analyzing the sequence reads comprises calculating a log2 effect size, wherein a positive number is an increase, and a negative number is a decrease.

117. The method of any one of claims 1-116, further comprising generating a DNA library from the cell-free DNA prior to the sequencing.

118. The method of claim 117, wherein the generating the DNA library comprises attaching an adapter to one or both ends of the DNA to produce adapted DNA.

119. The method of claim 89, wherein the medicament comprises an aminosalicylate, a mesalamine, a 5-aminosalicylic acid (5-ASA), a steroid, a prednisolone, a thiopurine, a JAK inhibitor, an anti-TNF antibody, a TNF inhibitor, a ustekinumab, a tofacitinib, an infliximab, a golimumab, a vedolizumab, a mirikizumab, a a4p7 integrin, an IL- 12 cytokine, an IL-23 cytokine, a small molecule targeting sphingosine- 1 -phosphate, or any combination thereof.

120. The method of any one of the preceding claims, wherein, prior to (b), the subject is determined to have IBD with an unknown subtype.

121. The method of any one of claims 1-120, wherein the subject has previously had an endoscopy procedure.

122. The method of claim 121, wherein the endoscopy procedure indicated that the subject had indeterminate colitis.

123. The method of any one of the preceding claims, wherein the cfNA comprises cfDNA.

124. The method of any of one of the preceding claims, wherein the cfNA comprises cfRNA, mRNA, or a combination thereof.

125. The method of any of one of the preceding claims, wherein the cfNA comprises bacterial cfNA, fungal cfNA, parasitic cfNA, viral cDNA, or any combination thereof.

126. The method of any one of the preceding claims, wherein the cfNA is not mitochondrial DNA.

127. The method of any one of the preceding claims, wherein the method does not comprise analysis of total cfNA, total subject cfNA, total mcfNA, or any combination thereof.

128. The method of any one of the preceding claims, wherein the cfNA does not comprise fetal nucleic acids.

129. The method of any one of the preceding claims, wherein the subject is not a transplant recipient.

130. The method of any one of the preceding claims, wherein the cfNA does not comprise a mixture of donor-derived cfDNA and host-derived cfDNA.

131. The method of any one of the preceding claims, wherein the method further comprises analyzing a genetic locus in the mcfNA or the subject cfNA, or a combination thereof.

132. The method of any one of the preceding claims, further comprising analyzing a genetic locus within a human genome.

133. The method of any one of claims 1-132, wherein the method comprises detecting:(a) a relative enrichment, wherein a relative enrichment comprises a peak-to-flank ratio of at least 0.1;(b) a relative depletion, wherein the relative depletion comprises a trough-to-flank ratio of at least 0.1; or(c) a combination of (a) and (b).

134. The method of any one of claims 1-133, wherein the method comprises distinguishing between the subject having Crohn’s disease and being healthy based at least in part on detecting:(a) a relative enrichment of GPIHBP1, SLC6A4, ZCWPW1, LINC00482, FENDRR, or any combination thereof;(b) a relative depletion of C3, SNURF, SNRPN, NM_001371415, ACE2, or any combination thereof; or(c) any combination of (a) and (b).

135. The method of any one of claims 1-134, wherein the method comprises distinguishing between the subject having Ulcerative colitis and being healthy based at least in part on detecting:(a) a relative enrichment of ACE2, C3, NM_001371415, SNURF, TMEM259, or any combination thereof;(b) a relative depletion of LINC00482, NR2F1, FENDRR, APOH, SLC6A4, or any combination thereof; or(c) any combination of (a) and (b).

136. The method of any one of claims 1-135, wherein the method comprises distinguishing between the subject having Ulcerative colitis and having Crohn’s disease based at least in part on detecting:(a) a relative enrichment of HTT, PDGFA, HRAT92, MS4A10, KANK2, or any combination thereof;(b) a relative depletion of SNORA23, AIF1, FANCF, ASF1B, TMEM259, or any combination thereof; or(c) any combination of (a) and (b).

137. The method of any one of claims 1-136, wherein the method comprises distinguishing between the subject having mild Ulcerative colitis and having moderate Ulcerative colitis based at least in part on detecting:(a) a relative enrichment of RHO, CASC4, KLK9, HSPA12B, NM 001371415, or any combination thereof;(b) a relative depletion of HCN2, LINC01410, MBNL3, PUS1, LTBP3, or any combination thereof; or(c) any combination of (a) and (b).

138. The method of any one of claims 1-137, wherein the method comprises distinguishing between the subject having mild Ulcerative colitis and being in remission for Ulcerative colitis based at least in part on detecting:(a) a relative enrichment of MIA3, RHO, 0LIG2, MAML3, SDC2, or any combination thereof;(b) a relative depletion of HCN2, TBX10, RUBCNL, KANK2, ARHGEF18, or any combination thereof; or(c) any combination of (a) and (b).

139. The method of any one of claims 1-138, wherein the method comprises distinguishing between the subject having mild Ulcerative colitis and having severe Ulcerative colitis based at least in part on detecting:(a) a relative enrichment of GDPD5, FBXO27, FAM110C, GFI1B, IFI27L2, or any combination thereof;(b) a relative depletion of NM 001371343, DNAJB8-AS1, EYS, TPSB2, TTLL10, or any combination thereof; or(c) any combination of (a) and (b).

140. The method of any one of claims 1-139, wherein the method comprises distinguishing between the subject having moderate Ulcerative colitis and being in remission for Ulcerative colitis based at least in part on detecting:(a) a relative enrichment of ARHGAP33, KDM1 A, MYB, SDC2, RPS6KA2, or any combination thereof;(b) a relative depletion of SIDT1, RUBCNL, DMRTB1, TMEM143, E2F3, or any combination thereof; or(c) any combination of (a) and (b).

141. The method of any one of claims 1-140, wherein the method comprises distinguishing between the subject having moderate Ulcerative colitis and having severe Ulcerative colitis based at least in part on detecting:(a) a relative enrichment of HPSE, ANGPTL4, HSPB2-C 11 orf52, IFI27L2, KLHL22, or any combination thereof;(b) a relative depletion of ADAMTS14, TBX15, MY018B, NM_001371417, SLC22A18AS, or any combination thereof; or(c) any combination of (a) and (b).

142. The method of any one of claims 1-141, wherein the method comprises distinguishing between the subject having severe Ulcerative colitis and being in remission for Ulcerative colitis based at least in part on detecting:(a) a relative enrichment of EX0C2, IGSF3, PTGIS, ECHS1, H0XC8, or any combination thereof;(b) a relative depletion of DNAJB8-AS, DMRTB1, MS4A10, MY018B, C8orf74, or any combination thereof; or(c) any combination of (a) and (b).

143. The method of any one of claims 1-142, wherein the method comprises distinguishing between the subject having mild Crohn’s disease and having moderate Crohn’s disease based at least in part on detecting a relative enrichment of POP7, FGF6, or a combination thereof.

144. The method of any one of claims 1-143, wherein the method comprises distinguishing between the subject having mild Crohn’s disease and being in remission for Crohn’s disease based at least in part on detecting a relative enrichment of ST8SIA2, TNKS1BP1, POP7, or any combination thereof.

145. The method of any one of claims 1-144, wherein the method comprises distinguishing between the subject having mild Crohn’s disease and having severe Crohn’s disease based at least in part on detecting:(a) a relative enrichment of SMYD4, LPCAT2, AADACL3, DPYSL5, TDRP, LOCI 00240728, or any combination thereof;(b) a relative depletion of SOX11, HSPB9, MIR378I, GAL3ST4, or any combination thereof; or(c) any combination of (a) and (b).

146. The method of any one of claims 1-145, wherein the method comprises distinguishing between the subject having moderate Crohn’s disease and being in remission for Crohn’s disease based at least in part on detecting a relative enrichment of MUC12, NAA40, UBE2E2-AS1, MHENCR, UBE2E2, or any combination thereof.

147. The method of any one of claims 1-146, wherein the method comprises distinguishing between the subject having moderate Crohn’s disease and having severe Crohn’s disease based at least in part on detecting:(a) a relative enrichment of KPTN, SHISA5, PRSS38, SLCO2A1, AMDHD2, ST8SIA2, or any combination thereof;(b) a relative depletion of S0X11, CLEC4G, MIR378I, or any combination thereof; or(c) any combination of (a) and (b).

148. The method of any one of claims 1-147, wherein the method comprises distinguishing between the subject having severe Crohn’s disease and being in remission for Crohn’s disease based at least in part on detecting:(a) a relative enrichment of ST8SIA2, CLIP3, LOC101929243, AMDHD2, UBE2E2, or any combination thereof(b) a relative depletion of GAL3ST4, CLEC4G, MIR378I, HSPB9, SOX11, or any combination thereof; or(c) any combination of (a) and (b).

149. A system configured to perform any one of the methods of claims 1-148.

150. The system of claim 149, wherein the system is configured to present a result of the analysis of the sequence reads to the healthcare provider.

151. The system of claim 150, wherein the system is configured to provide the healthcare provider with a clinical interpretation of the result of the analysis of the sequence reads.

152. The system of claim 151, wherein the clinical interpretation of the result of the analysis of the sequence reads comprises that the patient has ulcerative colitis, Crohn’s disease, or any other IBD syndrome or disease.

153. The system of any one of claims 149-153, wherein the system is configured to recommend to the healthcare provider an administration of a therapy for the disease.

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