Microbiome impact in metabolic disorder

Abstract

The present invention provides methods of treating, determining a predisposition to, diagnosing a metabolic disorder in a subject comprising detecting a microbiome of the gut in a sample from the subject; detecting a difference in gut microbial composition of the subject compared to a reference subject; administering to the subject a microbial modulator.

Description

MICROBIOME IMPACT IN METABOLIC DISORDERCROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of priority under 35 U.S.C. § 119(e) to U.S. Provisional Application No. 63 / 636,031 , filed April 18, 2024. The content of the prior application is considered part of and is hereby incorporated by reference in its entirety.BACKGROUND OF THE INVENTIONFIELD OF THE INVENTION

[0002] The present disclosure relates generally to methods of diagnosing and treating a metabolic disorder and more specifically to analyzing the microbial composition of the gut microbiome to diagnose and treat metabolic disorder.BACKGROUND INFORMATION

[0003] Obesity is a comprehensive medical condition that needs a multidimensional approach for long-term sustainable results. Eating, processing, and absorbing are all connected to the gut and the microbiome.

[0004] The gut microbiome is a complex community of trillions of microorganisms, including bacteria, viruses, fungi, and parasites, which reside in the digestive tract. This microbiome plays a crucial role in various aspects of health such as digestive health, immune system, mental health, and metabolic health. Short-chain fatty acids (SCFAs) are crucial compounds produced in the gut through the fermentation of dietary fiber by beneficial bacteria. They play a significant role in maintaining gut health and overall well-being. SCFAs nourish the cells lining the intestines, help maintain the integrity of the gut barrier and support a balanced gut microbiome. SCFAs also influence energy balance, blood glucose levels, and lipid metabolism.

[0005] The process of transport or diffusion of SCFAs within host cells occurs in their metabolism and / or hindrance of Histone deacetylases (HD AC) activity. The influence of SCFAs on enhanced epithelial barrier function and immune tolerance is complex and promotes gut homeostasis through multiple mechanisms, namely enhanced generation of mucus by intestinal goblet cells, the repression of nuclear factor-KB (NF-KB), the activation of inflammasomes, the generation of interleukin- 18 (IL- 18); augmented discharge of secretory IgA (slgA) by B cells, decreasing the expression of T cell-activating molecules on antigen-presenting cells, such as dendritic cells (DCs); and increasing the number and function of colonic regulatory T (Treg) cells, including the expression of FOXP3 and generation of anti-inflammatory cytokines (transforming growth factor-^ (TGFfl) and interleukin 10 (IL-10)).

[0006] There is a need for precision medicine approaches to save patients long-term expenses and a need for design of more tailored solutions to deliver the highest level of care.SUMMARY OF THE INVENTION

[0007] The present disclosure is based on the seminal discovery that the microbial composition of the gut of subjects with a metabolic disorder differs from that of a healthy subject. Specifically, the microbial composition of obese subjects display decreased alpha diversity of the gut microbiome, decreased SCFA producing microbes, increased gas producing microbes, and increased pathogenic microbes.

[0008] In one embodiment, the present disclosure provides a method of treating a metabolic disorder in a subject including: detecting a microbial composition of a gut microbiome in a sample from the subject; detecting a difference in the microbial composition of the subject compared to a reference subject; administering to the subject a microbial modulator; thereby treating the metabolic disorder in the subject.

[0009] In some aspects, detecting the microbial composition includes detecting microbiome diversity, a SCFA producing microbe, a gas producing microbe, a microbe associated metabolic pathway, a pathogenic microbe, or a combination thereof.

[0010] In some aspects, detecting the microbial composition includes sequencing microbial DNA from the sample from the subject. In one aspect, the sequencing the microbial DNA includes whole genome sequencing.

[0011] In some aspects, detecting microbiome diversity includes detecting alpha microbial diversity, beta microbial diversity, or a combination thereof.

[0012] In one aspect, the alpha microbial diversity in the sample from the subject is reduced compared alpha microbial diversity in a sample from the reference subject.

[0013] In one aspect detecting the alpha microbial diversity includes using Shannon Diversity Index.

[0014] In some aspects, the beta microbial diversity in the subject is increased compared beta microbial diversity in the reference subject.

[0015] In one aspect, relative abundance of the SCFA producing microbe in the subject is increased compared to relative abundance of the SCFA producing microbe in the reference subject.

[0016] In some aspects, the number of the SCFA producing microbe in the sample from the subject is decreased compared to number of the SCFA producing microbe in a sample from the reference subject.

[0017] In some aspects, the SCFA producing microbe includes faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, anaerostipes, dialister, flavonifractior, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

[0018] In one aspect, the SCFA producing microbe includes faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

[0019] In one aspect, relative abundance of the gas producing microbe in the subject is increased compared to relative abundance of the gas producing microbe in the reference subject.

[0020] In some aspects, the gas producing microbe includes bacteroides fragilis, escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, methanobrevibacter oralis, or a combination thereof. In one aspect, the gas producing microbe includes escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, or a combination thereof.

[0021] In one aspect, relative abundance of a microbe associated metabolic pathway in the subject is increased compared to relative abundance of the microbe associated metabolic pathway in the sample from the reference subject.

[0022] In some aspects, the metabolic pathway is methanogenesis from H2 and CO2; methanogenesis from acetate; assimilatory sulfate reduction I; superpathway of sulfate assimilation and cysteine biosynthesis; L-lysine biosynthesis; preQO biosynthesis, pyrimidine deoxyribonucleosides salvage; superpathway of polyamine biosynthesis I; CMP-3-3deoxy-D- manno-octulosonate biosynthesis, incomplete reductive TCA cycle; pyrimidine deoxyribonucleotide phosphorylation; superpathway of pyrimidine ribonucleotides de novo biosynthesis; superpathway of guanosine nucleotides de novo biosynthesis I; hexitol fermentation to lactate, formate, ethanol, and acetate; glycogen biosynthesis I (from ADP-D-Glucose); or a combination thereof. In one aspect, the metabolic pathway is pyrimidine deoxyribonucleotide phosphorylation.

[0023] In one aspect, the relative abundance of the pathogenic microbe in the subject is increased compared to the relative abundance of the pathogenic microbe in the reference subject.

[0024] In some aspects, a number of the pathogenic microbe in the sample from the subject is increased compared to a number of the pathogenic microbe in a sample from the reference subject.

[0025] In some aspects, the pathogenic microbe includes klebsiella, enterobacter, shigella, salmonella, citrobacter, serratia, proteus, or a combination thereof. In one aspect, the pathogenic microbe includes klebsiella, shigella, salmonella, or a combination thereof.

[0026] In some aspects, the reference subject is a healthy subject or the subject at an earlier time point.

[0027] In some aspects, the sample includes a fecal sample, a mucosal, sample, a rectal swab, an intestinal fluid sample, or a combination there of. In one aspect, the sample includes a fecal sample.

[0028] In some aspects, the microbial modulator includes a probiotic, a prebiotic, a special diet, a supplement, a functional food, an SCFA production modulator, a gut homeostasis modulator, a GLP-1 hormone secretion modulator, or a combination thereof. In one aspect, the probiotic is a combination probiotic.

[0029] In some aspects, the special diet includes a high fiber diet, a high potassium diet, a vegetable-rich diet, a fruit-rich diet, a carbohydrate-rich diet, or a combination thereof. In one aspect, the high potassium diet includes a banana, an apricot, a peach, or a combination thereof. In one aspect, the vegetable-rich diet includes a lettuce, a tomato, a zucchini, an okra, or a combination thereof. In one aspect, the fruit-rich diet includes a cantaloupe, a grape, a berry, a cherry, an avocado, an olive, or a combination thereof. In one aspect, the carbohydrate-rich diet includes gluten-free bread, rice bread, rice, or a combination thereof. In one aspect, the supplement includes bifidobacterium breve SG05, lactobacillus rhamnosus SGI 6, lactococcus lactis SGI 4, bifidobacterium bifidum SG28, flaxseed powder, turmeric, bifidobacterium infantis SG25, limosilactobacillius reuteri SG01, lactobacillus paracasei SGI 7, bifidobacterium longum SGO, lactobacillus delbrueckii subsp. bulgaricus SG10, lactobacillus plantarum SGO6, bifidobacterium breve SG05, lactobacillus rhamnosus SG16, lactobacillus rhamnosus SG21, bifidobacterium bifidum SG28, or a combination thereof.In some aspects, the metabolic disorder includes diabetes, obesity, phenylketonuria (PKU), Gaucher’s disease, hemochromatosis, mitochondrial disorders, hyperthyroidism, hypothyroidism, Wilson’s disease, maple syrup urine disease (MSUD), galactosemia, or a combination thereof.

[0030] In one embodiment, the present disclosure provides a method of stratifying subjects for administration of a microbial modulator including: a) detecting a microbial composition of a gut microbiome in a sample from the subject; b) detecting a difference in the microbial composition of the subject compared to a reference subject; c) stratifying the subject based on the difference inthe microbial composition; d) administering a microbial modulator to the subject based on the stratification in (c).

[0031] In one embodiment, the present disclosure provides a method of determining a predisposition to or diagnosing a metabolic disorder in a subject including: detecting a microbial composition of a gut microbiome in a sample from the subject; detecting a difference in the microbial composition of the subject compared to a reference subject, wherein the difference in the microbial composition of the subject compared to the reference subject is indicative of predisposition to or presence of the metabolic disorder; thereby determining a predisposition to or diagnosing the metabolic disorder in the subject.BRIEF DESCRIPTION OF THE DRAWINGS

[0032] FIG. 1 is a schematic diagram illustrating the consequence modulating SCFA producing microbes in the gut.

[0033] FIG. 2 is a graph illustrating changes in Shannon Diversity Index in an obesity cohort compared to a healthy subject. P< 0.05; **, P < 0.01; ***, P < 0.001; ****, P< 0.0001.

[0034] FIG. 3 is a graph illustrating a principal coordinates Analysis (PCoA) in the obesity cohort vs the healthy cohort.

[0035] FIG. 4 is a graph illustrating relative abondance of SCFA producing microbes in the obesity cohort vs the healthy cohort.

[0036] FIG. 5 is a graph illustrating relative abondance of gas producing microbes in the obesity cohort vs the healthy cohort.

[0037] FIG. 6 is a graph illustrating pathway analysis in the obesity cohort vs the healthy cohort.

[0038] FIG. 7 is graph illustrating relative abondance of pathogenic microbes in the obesity cohort vs the healthy cohort.

[0039] FIG. 8 is a graph illustrating random forest analysis.

[0040] FIG. 9 is a schematic diagram illustrating the role of high fiber in regulating metabolic health pathways in obesity.

[0041] The figures described herein are for illustrative purposes only and are not drawn to scale.DETAILED DESCRIPTION OF THE INVENTION

[0042] The present disclosure is based on the seminal discovery that the microbial composition of the gut of subjects with a metabolic disorder differs from that of a healthy subject. Specifically, the microbial composition of obese subjects display decreased alpha diversity of the gutmicrobiome, decreased SCFA producing microbes, increased gas producing microbes, and increased pathogenic microbes.

[0043] Before the present systems and methods are described, it is to be understood that this invention is not limited to the particular systems, methods, and experimental conditions described, as such systems, methods, and conditions may vary. It is also to be understood that the terminology used herein is for the purposes of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only in the appended claims.

[0044] As used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, references to “the method” include one or more methods, and / or steps of the type described herein which will become apparent to those persons skilled in the art upon reading this disclosure and so forth.

[0045] As used herein, the term “and / or” includes any and all combinations of one or more of the associated listed items.

[0046] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the invention, it will be understood that modifications and variations are encompassed within the spirit and scope of the instant disclosure. The preferred methods and materials are now described.

[0047] In one embodiment, the present disclosure provides a method of treating a metabolic disorder in a subject including: detecting a microbial composition of a gut microbiome in a sample from the subject; detecting a difference in the microbial composition of the subject compared to a reference subject; administering to the subject a microbial modulator; thereby treating the metabolic disorder in the subject.

[0048] The term “metabolic disorder” refers to a condition that disrupts normal metabolic processes in the body. These processes involve the biochemical reactions that convert food into energy and other necessary substances. Examples of metabolic disorders may include but are not limited to diabetes, obesity, phenylketonuria (PKU), Gaucher’s disease, hemochromatosis,mitochondrial disorders, hyperthyroidism, hypothyroidism, Wilson’s disease, maple syrup urine disease (MSUD), and galactosemia.

[0049] The term “microbiome” refers to the community of microorganisms, including bacteria, fungi, viruses, and other microbes, which inhabit a particular environment. The term “microbiome of the gut” refers to the community of microorganisms, including bacteria, fungi, viruses, and other microbes, which live in the digestive tract. The gut microbiome consists of trillions of microbes. There are over a thousand species of bacteria in the human gut, each playing different roles in maintaining health. Microbes help break down complex carbohydrates and dietary fibers that the human body cannot digest on its own. Microbes produce short-chain fatty acids, which are crucial for gut health. The microbiome of the gut influences metabolism and can affect body weight and the risk of metabolic diseases. The gut microbial composition refers to the variety and abundance of microorganisms residing in the digestive tract.

[0050] The term “subject” as used herein refers to any individual or patient to which the subject methods are performed. Generally, the subject is human, although as will be appreciated by those in the art, the subject may be a non-human animal. Thus, other animals, including vertebrate such as rodents (including mice, rats, hamsters and guinea pigs), cats, dogs, rabbits, farm animals including cows, horses, goats, sheep, pigs, chickens, and non-human primates (including monkeys, chimpanzees, orangutans and gorillas) are included within the definition of subject.

[0051] The terms “treat”, “treatment”, and “treating” refer to the reduction of the severity, duration, or progression of a disease or disorder or one or more symptoms associated with a disease or disorder.

[0052] the term “detecting” refers to the process of identifying and measuring the presence, quantity, interaction, and / or activity of biological molecules. Detecting can involve various techniques and tools including but is not limited to microscopy, polymerase chain reaction (PCR), immunoassays, biosensors, coimmunoprecipitation (Co-IP), dTAG degradation, Western blotting, DNA sequencing, bioinformatics analysis, platform sever analysis, machine learning based approach, cell viability assay, Python, NeXtProt server.

[0053] For the methods disclosed herein, the sample from the subject can be any biological sample derived from the subject that contains microbes. The sample can include fecal sample, a mucosal, sample, a rectal swab, and an intestinal fluid sample.

[0054] The terms “administration of’ and or “administering” should be understood to mean providing a microbial modulator in a therapeutically effective amount to the subject in need of treatment. Administration routes can be enteral, topical or parenteral. As such, administrationroutes include but are not limited to intracutaneous, subcutaneous, intravenous, intraperitoneal, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, transdermal, transtracheal, subcuticular, intraarticulare, subcapsular, subarachnoid, intraspinal and intrasternal, oral, sublingual buccal, rectal, vaginal, nasal ocular administrations, as well infusion, inhalation, and nebulization. The phrases “parenteral administration” and “administered parenterally” as used herein means modes of administration other than enteral and topical administration. Routes of administration may include but are not limited to inhalation, otic, buccal, conjunctival, dental, endocervical, endosinusial, endotracheal, enteral, epidural, extra-amniotic, extracorporeal, hemodialysis, infiltration, interstitial, intraabdominal, intraamniotic, intraarterial, intraarticular, intrabiliary, intrabronchial, intrabursal, intracardiac, intracartilaginous, intracaudal, intracavemous, intracavitary, intracerebroventricular, intracisternal, intracorneal, intracoronal, intracoronary, intracorpous cavemaosum, intradermal, intradiscal, intraductal, intraduodenal, intradural, intraepidermal, intraesophageal, intragastric, intragingival, intrahippocampal, intraileal, intralesional, intraluminal, intralymphatic, intramedullary, intrameningeal, intramuscular, intraocular, intraovarian, intrapericardial, intraperitoneal, intrapleural, intraprostatic, intrapulmonary, intrasinal, intraspinal, intrasynovial, intratendinous, intratesticular, intrathoracic, intratubular, intratumor, intratympanic, intrauterine, intravascular, intravenous, intravenous bolus, intravenous drip, intravesical, intravitreal, iontophoresis, irrigation, laryngeal, nasal, nasogastric, ophthalmic, oral, oropharyngeal, parenteral, percutaneous, periarticular, peridural, perineural, periodontal, rectal, retrobulbar, subarachnoid, subconjunctival, subcutaneous, sublingual, submucosal, topical, transdermal, transmucosal, transplacental, transtracheal, transtympanic, ureteral, urethral, vaginal, infraorbital, intraparenchymal, intrathecal, intraventricular, stereotactic administration, or any combination thereof. The microbial modulator can be administered in a variety of unit dosage forms depending upon the method of administration. Suitable unit dosage forms include, but are not limited to powders, tablets, pills, capsules, lozenges, suppositories, patches, nasal sprays, injectables, implantable sustained-release formulations, lipid complexes.

[0055] In some aspects, detecting the microbial composition includes detecting microbiome diversity, a SCFA producing microbe, a gas producing microbe, a metabolic pathway associated microbe, a pathogenic microbe, or a combination thereof.

[0056] The term “microbiome diversity” refers to the variety and abundance of different microbial species within a specific environment, such as the human gut. Higher diversity is generally associated with better health and resilience against diseases. Microbiome diversity canbe categorized into several types such as alpha diversity, beta diversity, and gamma diversity, each providing different insights into microbial communities. Alpha diversity measures the diversity within a single sample or environment. The metrics for alpha diversity include but are not limited to richness (number of species) and evenness (distribution of species). Tools for measuring microbiome alpha diversity may include but are not limited to Shannon Diversity Index and Simpson’s Diversity Index. Alpha diversity may be used to assess the variety and abundance of microbial species in a specific sample, such as the gut. Beta diversity measures the differences in microbial composition between two or more samples or environments. Principal coordinates analysis (PCoA) is a technique used to visualize the differences in microbial communities based on beta diversity metrics. PCoA projects the distances onto a set of coordinate axes, typically selecting the first two axes that best preserve the original distances. The resulting plot shows the relative similarities or differences between samples, making it easier to interpret complex microbial data. Principal coordinate 1 (PCO1) and Principal coordinate 2 (PCO2) in microbiome analysis are the first two principal coordinates derived from Principal Coordinates Analysis (PCoA). PCO1 captures the largest amount of variance in the data. PCO1 represents the most significant differences between samples. Samples that are far apart along PCO1 are more dissimilar in terms of their microbial composition. PCO2 captures the second largest amount of variance. PCO2 represents the next most significant differences between samples. Samples that are far apart along PCO2 are also dissimilar, but in a different aspect compared to PCO1. In a PCoA plot, each point represents a sample, and the distances between points reflect the dissimilarities in microbial composition. Tools available for calculating beta diversity metrics in microbiome analysis may include but are not limited to QIIME 2, animalcules, and EzMAP.

[0057] The term “short-chain fatty acids” or “SCFAs” refer to fatty acids that are produced by certain gut microbes through the fermentation of dietary fibers. These SCFAs, including acetate, propionate, and butyrate, play crucial roles in maintaining gut health, modulating immune responses, and regulating metabolism. Examples of SCFA producing microbes may include but are not limited to faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, anaerostipes, dialister, flavonifractior, odoribacter, lactobacillus, butyricimonas, butyrivibrio, and butyricicoccus.

[0058] The term “gas-producing microbe” refers to a microbe that generate gas as a byproduct of its metabolic process. Examples of gas producing microbes may include but are not limited to bacteroides fragilis, escherichia coli, akkermanksia muciniphila, bifidobacteriumpseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, and methanobrevibacter oralis.

[0059] The term “metabolic pathway” refers to a series of chemical reactions within a cell that lead to the transformation of molecules. Metabolic pathways are crucial for maintaining cellular functions and overall homeostasis. Examples of metabolic pathways may include but are not limited to glycolysis, citric acid cycle (krebs cycle) such as oxidation of acetyl-CoA to CO2 and H2O; pentose phosphate pathway; fatty acid synthesis; beta-oxidation; cholesterol synthesis; amino acid synthesis; urea cycle; protein degradation; purine synthesis; pyrimidine synthesis; nucleotide salvage pathways; oxidative phosphorylation; photosynthesis, gluconeogenesis; glycogenolysis; glycogenesis; methanogenesis from H2 and CO2; methanogenesis from acetate; assimilatory sulfate reduction I; superpathway of sulfate assimilation and cysteine biosynthesis; L-lysine biosynthesis; preQO biosynthesis, pyrimidine deoxyribonucleosides salvage; superpathway of polyamine biosynthesis I; CMP-3-3deoxy-D-manno-octulosonate biosynthesis, incomplete reductive TCA cycle; pyrimidine deoxyribonucleotide phosphorylation; superpathway of pyrimidine ribonucleotides de novo biosynthesis; superpathway of guanosine nucleotides de novo biosynthesis I; hexitol fermentation to lactate, formate, ethanol, and acetate; and glycogen biosynthesis I (from ADP-D-Glucose).

[0060] The term “microbe-associated metabolic pathway” refers to the series of chemical reactions carried out by microorganisms (such as bacteria, archaea, fungi, and algae) to sustain their life processes. Microbes have diverse metabolic pathways that allow them to thrive in various environments. Examples of microbe associated metabolic pathways may include but are not limited to glycolysis; pentose phosphate pathway; entner-doudoroff pathway; beta-oxidation; fatty acid synthesis; amino acid catabolism; urea cycle; cellular respiration; fermentation; photosynthesis; methanogenesis; nitrogen fixation; sulfur cycle; carbon cycle; methanogenesis from H2 and CO2; methanogenesis from acetate; assimilatory sulfate reduction I; superpathway of sulfate assimilation and cysteine biosynthesis; L-lysine biosynthesis; preQO biosynthesis, pyrimidine deoxyribonucleosides salvage; superpathway of polyamine biosynthesis I; CMP-3- 3deoxy-D-manno-octulosonate biosynthesis, incomplete reductive TCA cycle; pyrimidine deoxyribonucleotide phosphorylation; superpathway of pyrimidine ribonucleotides de novo biosynthesis; superpathway of guanosine nucleotides de novo biosynthesis I; hexitol fermentation to lactate, formate, ethanol, and acetate; and glycogen biosynthesis I (from ADP-D-Glucose). The metabolic pathway associated microbes are microbes that are linked to these pathways.

[0061] The term “pathogenic microbe” refers to a microorganism that cause diseases in its host. Examples of pathogenic microbes include bacteria, viruses, fungi, and protozoa. Examples of pathogenic microbes may include but are not limited to klebsiella, enterobacter, shigella, salmonella, citrobacter, serratia, proteus, escherichia coli (E. coli), and giardia lamblia.

[0062] The term “microbial modulator” refers to a substance or intervention that influence the composition and activity of the microbiome. Examples of microbial modulators may include but are not limited to probiotics, prebiotics, diets, supplement, functional foods, SCFA production modulators gut homeostasis modulator, GLP-1 hormone secretion modulators, postbiotics, symbiotic, and pharmaceuticals.

[0063] In some aspects, detecting the microbial composition includes sequencing microbial DNA from the sample from the subject. Examples of sequencing may include but are not limited to sanger sequencing, maxam-gilbert sequencing, next-generation sequencing (NGS), pyrosequencing, targeted sequencing, RNA sequencing (RNA-Seq), bisulfite sequencing, metagenomic sequencing, de novo sequencing, exome sequencing, ChIP sequencing (ChlP-Seq), mate pair sequencing, paired-end sequencing, epigenomic sequencing, long read sequencing, cycle sequencing, RAD-Seq (restriction site-associated DNA sequencing), amplicon sequencing, shotgun sequencing, tilling sequencing, 3D sequencing, 4D sequencing, capture sequencing, CRISPR sequencing, whole-genome sequencing (WGS), microRNA sequencing, expression sequencing, MeDIP-Seq, RRB-sequencing, dP-Seq, sequencing for functional genomics, ATAC- Seq, pooled library sequencing, shallow sequencing, CAGE-Seq, Single-Cell Sequencing, CLIP- Seq, high-throughput sequencing, SOLiD sequencing, SMRT sequencing, MPSS, polony sequencing, solexa sequencing, ion torrent semi-conductor sequencing, DNA nanoball sequencing, sequencing by hybridization, and nanopore sequencing. In one aspect, the sequencing microbial DNA includes whole genome sequencing.

[0064] In some aspects, detecting microbiome diversity includes detecting alpha microbial diversity, beta microbial diversity, or a combination thereof.In one aspect, the alpha microbial diversity in the sample from the subject is reduced compared to alpha microbial diversity in a sample from the reference subject. For example, alpha microbial diversity in the sample from the subject is reduced or decreased compared to alpha microbial diversity in a sample from the reference subject. The reduction includes any reduction of the alpha microbial diversity (e.g., 1% reduction of the alpha microbial diversity), up to a complete reduction of the alpha microbial diversity (e.g., a 100% reduction of the alpha microbial diversity). The alpha microbial diversity can be reduced or decreased by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20,25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 05, 96, 97, 98, 99 or 100% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 1% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 5% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 10% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 15% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 20% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 25% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 30% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 35% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 40% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 45% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 50% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 55% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 60% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 65% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 70% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 75% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 80% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 85% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 90% compared to alpha microbial diversity in the sample from thereference subject. In one embodiment, the alpha microbial diversity can be reduced by 95% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 100% compared to alpha microbial diversity in the sample from the reference subject.

[0065] In one aspect detecting the alpha microbial diversity includes using Shannon Diversity Index.

[0066] The magnitude of changes in the Shannon Diversity Index can provide insights into the biodiversity of an ecosystem. A decrease in the index points to reduced diversity. For example, the Shannon Diversity Index measured in the sample from the subject is reduced or decreased compared to Shannon Diversity Index measured in a sample from the reference subject. The reduction includes any reduction of the Shannon Diversity Index (e.g., 1% reduction of the Shannon Diversity Index), up to a complete reduction of the Shannon Diversity Index (e.g., a 100% reduction of the Shannon Diversity Index). The Shannon Diversity Index can be reduced or decreased by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 05, 96, 97, 98, 99 or 100% compared to Shannon Diversity Index measured in the sample from the reference subject. . In one embodiment, the Shannon Diversity Index can be reduced by 1% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 5% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 10% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 15% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 20% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 25% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 30% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 35% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 40% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 45% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 50% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the ShannonDiversity Index is reduced by 55% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 60% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 65% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 70% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 75% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 80% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index can be reduced by 85% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 90% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 95% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 100% compared to Shannon Diversity Index in the sample from the reference subject.

[0067] In some aspects, the beta microbial diversity in the subject is increased compared to beta microbial diversity in the reference subject. For example, beta microbial diversity in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 0.5 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 1.5 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 3 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 5 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 10 times greater than the beta microbial diversity in a sample from a reference subject.

[0068] The term “relative abundance” refers to the proportion of a particular species or type within a community or ecosystem compared to the total number of species or types present. Relative abundance here refers to the proportion of a specific microbe or pathway relative to the total microbial community or total pathways.

[0069] In one aspect, the relative abundance of the SCFA producing microbe in the subject is increased compared to the relative abundance of the SCFA producing microbe in the reference subject. For example, the relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increase by at least 0.5 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbes in a sample from the subject may be increased by at least 3 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 5 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject.

[0070] In some aspects, the number of the SCFA producing microbe in the sample from the subject is decreased compared to number of the SCFA producing microbes in a sample from the reference subject. For example, the number of the SCFA producing microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the number of the SCFA producing microbe in a sample from a reference subject. Number of the SCFA producing microbes in a sample from the subject may be increase by at least 0.5 times greater than the number of the SCFA producing microbe in a sample from a reference subject. Number of the SCFA producing microbe in a sample from the subject may be increased by at least 1.5 times greater than the number of the SCFA producing microbe in a sample from a reference subject. Number of the SCFA producing microbes in a sample from the subject may be increased by at least 3 times greater than the number of the SCFA producing microbes in a sample from a reference subject. Number of the SCFA producing microbe in a sample from the subject may be increased by at least 5 times greater than the number of the SCFA producing microbe in a sample from a reference subject. The number of the SCFA producing microbes in a sample from the subject may be increased by at least 10 times greater than the number of the SCFA producing microbes in a sample from a reference subject.

[0071] In some aspects, the SCFA producing microbe includes faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, anaerostipes, dialister, flavonifractior, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

[0072] In one aspect, the SCFA producing microbe includes faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

[0073] In one aspect, the relative abundance of the gas producing microbe in the subject is increased compared to the relative abundance of the gas producing microbe in the reference subject. For example, the relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 0.5 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 3 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 5 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbes in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject.

[0074] In some aspects, the gas producing microbe includes bacteroides fragilis, escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, methanobrevibacter oralis, or a combination thereof. In one aspect, the gas producing microbe includes escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, or a combination thereof.

[0075] In one aspect, the relative abundance of the microbe associated metabolic pathway in the subject is increased compared to the relative abundance of the microbe associated metabolic pathway in the sample from the reference subject. For example, the relative abundance of themetabolic pathway in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundance of the metabolic pathway microbe in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 0.5 times greater than the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 3 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 5 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject.

[0076] In some aspects, the metabolic pathway is methanogenesis from H2 and CO2; methanogenesis from acetate; assimilatory sulfate reduction I; superpathway of sulfate assimilation and cysteine biosynthesis; L-lysine biosynthesis; preQO biosynthesis, pyrimidine deoxyribonucleosides salvage; superpathway of polyamine biosynthesis I; CMP-3-3deoxy-D- manno-octulosonate biosynthesis, incomplete reductive TCA cycle; pyrimidine deoxyribonucleotide phosphorylation; superpathway of pyrimidine ribonucleotides de novo biosynthesis; superpathway of guanosine nucleotides de novo biosynthesis I; hexitol fermentation to lactate, formate, ethanol, and acetate; glycogen biosynthesis I (from ADP-D-Glucose); or a combination thereof. In one aspect, the pathway is pyrimidine deoxyribonucleotide phosphorylation.

[0077] In one aspect, the relative abundance of the pathogenic microbe in the subject is increased compared to the relative abundance of the pathogenic microbe in the reference subject. For example, the relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 0.5 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased byat least 3 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 5 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject.

[0078] In some aspects, the number of the pathogenic microbes in the sample from the subject is increased compared to number of the pathogenic microbe in a sample from the reference subject. For example, the number of pathogenic microbes in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the number of the pathogenic microbe in a sample from a reference subject. The number of the pathogenic microbes in a sample from the subject may be increased by at least 0.5 times greater than the number of the pathogenic microbe in a sample from a reference subject. The number of the pathogenic microbes in a sample from the subject may be increased by at least 1.5 times greater than the number of the pathogenic microbe in a sample from a reference subject. Number of the pathogenic microbe in a sample from the subject may be increased by at least 3 times greater than the number of the pathogenic microbe in a sample from a reference subject. The number of pathogenic microbes in a sample from the subject may be increased by at least 5 times greater than the number of the pathogenic microbes in a sample from a reference subject. The number of the pathogenic microbes in a sample from the subject may be increased by at least 10 times greater than the number of the pathogenic microbe in a sample from a reference subject.

[0079] In some aspects, the pathogenic microbe includes klebsiella, enterobacter, shigella, salmonella, citrobacter, serratia, proteus, or a combination thereof. In one aspect, the pathogenic microbe is klebsiella, shigella, salmonella, or a combination thereof.

[0080] In some aspects, the reference subject includes a healthy subject or the subject at an earlier time point.

[0081] As used herein the term “healthy subject” refers to a subject who does not have a metabolic disorder. The term “the subject at an earlier time point” refers to the subject with the metabolic disorder at an earlier time point than when the treatment, diagnosis, or stratification was performed.

[0082] In some aspects, the sample includes a fecal sample, a mucosal, sample, a rectal swab, an intestinal fluid sample, or a combination there of. In one aspect, the sample includes a fecal sample.

[0083] In some aspects, the microbial modulator includes a probiotic, a prebiotic, a special diet, a supplement, a functional food, an SCFA production modulator, a gut homeostasis modulator, a GLP-1 hormone secretion modulator, or a combination thereof. In one aspect, the probiotic is a custom probiotic.

[0084] The term “probiotic” refers to live microorganisms, often referred to as “good” or “helpful” bacteria, that provide health benefits when consumed in adequate amounts. Examples of probiotic include but are not limited to lactobacillus acidophilus, lactobacillus rhamnosus, lactobacillus casei, bifidobacterium, bifidobacterium bifidum, bifidobacterium longum, bifidobacterium lactis, saccharomyces boulardii, yogurt, kefir, sauerkraut, kimchi, miso, tempeh, buttermilk, pickles, kombucha, fermented cheeses; probiotic supplements such as capsules and tablets, powders and liquids.

[0085] The term “prebiotic” refers to a type of non-digestible food ingredient that promotes the growth and activity of beneficial bacteria in the gut. Unlike probiotics, which are live bacteria, prebiotics serve as food for these bacteria, helping them thrive and maintain a healthy gut environment. Examples of prebiotics include but are not limited to chicory root, dandelion greens, Jerusalem artichoke, garlic, onions, leeks, asparagus, bananas, barley, oats, apples, konjac root, cocoa, burdock root, flaxseeds, yacon root, jicama root, wheat bran, seaweed, avocado.

[0086] The term “supplement” refers to a product designed to augment a subject’s diet and provide nutrients that the subject might not get enough of from food alone. Supplements come in various forms, including but are not limited to tablets, capsules, powders, and liquids. Examples of supplements include but are not limited to vitamins, minerals, herbs, botanicals, amino acids, enzymes, probiotic, bifidobacterium breve SG05, lactobacillus rhamnosus SGI 6, lactococcus lactis SG14, bifidobacterium bifidum SG28, flaxseed powder, turmeric, bifidobacterium infantis SG25, limosilactobacillius reuteri SG01, lactobacillus paracasei SGI 7, bifidobacterium longum SGO, lactobacillus delbrueckii subsp. bulgaricus SG10, lactobacillus plantarum SGO6, bifidobacterium breve SG05, lactobacillus rhamnosus SG16, lactobacillus rhamnosus SG21, and bifidobacterium bifidum SG28.

[0087] The term “functional food” refers to foods that offer health benefits beyond their basic nutritional value. Functional foods can help prevent nutrient deficiencies, protect against diseases, and promote overall health and well-being. Functional foods are generally categorized into two types: conventional and modified. Examples of functional food include but are not limited to fruits, vegetables, nuts, Seeds, legumes, whole grains, seafood, fermented foods, fortified juices, fortified dairy products, and fortified grains.

[0088] Examples of SCFA production modulator include but are not limited to high fiber diets such as oats, chia seeds, flaxseeds; fermented foods such as yogurt, kimchi, kefir; prebiotics such as garlic, onions, bananas; and supplements.

[0089] The term “gut homeostasis modulator” refers to any substance, intervention, or strategy that helps maintain or restore the balance and health of the gut microbiota. Examples of gut homeostasis modulators include but are not limited to prebiotics, probiotics, dietary fiber, regular exercise, stress management, and supplements.

[0090] The term “Glucagon-like peptide- 1” or “GLP-1” refers to an incretin hormone that plays a crucial role in regulating blood glucose levels by enhancing insulin secretion. Examples of GLP- 1 modulators include but are not limited to high fiber foods, healthy fats, protein-rich foods, oats, barley, legumes, avocados, nuts, eggs, fish, regular physical activity, stress management, probiotic supplements, and prebiotic supplements.

[0091] In some aspects, the diet includes a high fiber diet, a high potassium diet, a vegetablerich diet, a fruit-rich diet, a carbohydrate-rich diet, or a combination thereof. In one aspect, the high potassium diet includes a banana, an apricot, a peach, or a combination thereof. In one aspect, the vegetable-rich diet includes a lettuce, a tomato, a zucchini, an okra, or a combination thereof. In one aspect, the fruit-rich diet includes a cantaloupe, a grape, a berry, a cherry, an avocado, an olive, or a combination thereof. In one aspect, the carbohydrate-rich diet includes gluten-free bread, rice bread, rice, or a combination thereof. In one aspect, the supplement includes bifidobacterium breve SG05, lactobacillus rhamnosus SGI 6, lactococcus lactis SGI 4, bifidobacterium bifidum SG28, flaxseed powder, turmeric, bifidobacterium infantis SG25, limosilactobacillius reuteri SG01, lactobacillus paracasei SGI 7, bifidobacterium longum SGO, lactobacillus delbrueckii subsp. bulgaricus SG10, lactobacillus plantarum SGO6, bifidobacterium breve SG05, lactobacillus rhamnosus SG16, lactobacillus rhamnosus SG21, bifidobacterium bifidum SG28, or a combination thereof.

[0092] In some aspects, the metabolic disorder includes diabetes, obesity, phenylketonuria (PKU), Gaucher’s disease, hemochromatosis, mitochondrial disorders, hyperthyroidism, hypothyroidism, Wilson’s disease, maple syrup urine disease (MSUD), galactosemia, or a combination thereof.

[0093] In one aspect, the metabolic disorder include diabetes, obesity, or a combination thereof.

[0094] In one embodiment, the present disclosure provides a method of stratifying subjects for administration of a microbial modulator including: a) detecting a microbial composition of a gut microbiome in a sample from the subject; b) detecting a difference in the microbial compositionof the subject compared to a reference subject; c) stratifying the subject based on the difference in the microbial composition; d) administering a microbial modulator to the subject based on the stratification in (c).

[0095] In some aspects, detecting the microbial composition includes sequencing microbial DNA from the sample from the subject. Examples of sequencing may include but are not limited to sanger sequencing, maxam-gilbert sequencing, next-generation sequencing (NGS), pyrosequencing, targeted sequencing, RNA sequencing (RNA-Seq), bisulfite sequencing, metagenomic sequencing, de novo sequencing, exome sequencing, ChIP sequencing (ChlP-Seq), mate pair sequencing, paired-end sequencing, epigenomic sequencing, long read sequencing, cycle sequencing, RAD-Seq (restriction site-associated DNA sequencing), amplicon sequencing, shotgun sequencing, tilling sequencing, 3D sequencing, 4D sequencing, capture sequencing, CRISPR sequencing, whole-genome sequencing (WGS), microRNA sequencing, expression sequencing, MeDIP-Seq, RRB-sequencing, dP-Seq, sequencing for functional genomics, ATAC- Seq, pooled library sequencing, shallow sequencing, CAGE-Seq, Single-Cell Sequencing, CLIP- Seq, high-throughput sequencing, SOLiD sequencing, SMRT sequencing, MPSS, polony sequencing, solexa sequencing, ion torrent semi-conductor sequencing, DNA nanoball sequencing, sequencing by hybridization, and nanopore sequencing. In one aspect, the sequencing microbial DNA includes whole genome sequencing.

[0096] In some aspects, detecting microbiome diversity includes detecting alpha microbial diversity, beta microbial diversity, or a combination thereof.In one aspect, the alpha microbial diversity in the sample from the subject is reduced compared to alpha microbial diversity in a sample from the reference subject. For example, alpha microbial diversity in the sample from the subject is reduced or decreased compared to alpha microbial diversity in a sample from the reference subject. The reduction includes any reduction of the alpha microbial diversity (e.g., 1% reduction of the alpha microbial diversity), up to a complete reduction of the alpha microbial diversity (e.g., a 100% reduction of the alpha microbial diversity). The alpha microbial diversity can be reduced or decreased by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 05, 96, 97, 98, 99 or 100% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 1% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 5% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 10% compared to alpha microbialdiversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 15% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 20% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 25% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 30% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 35% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 40% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 45% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 50% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 55% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 60% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 65% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 70% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 75% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 80% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 85% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 90% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 95% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 100% compared to alpha microbial diversity in the sample from the reference subject.

[0097] In one aspect, detecting the alpha microbial diversity includes using Shannon Diversity Index. For example, the Shannon Diversity Index measured in the sample from the subject isreduced or decreased compared to Shannon Diversity Index measured in a sample from the reference subject. The reduction includes any reduction of the Shannon Diversity Index (e.g., 1% reduction of the Shannon Diversity Index ), up to a complete reduction of the Shannon Diversity Index (e.g., a 100% reduction of the Shannon Diversity Index ). The Shannon Diversity Index can be reduced or decreased by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 05, 96, 97, 98, 99 or 100% compared to Shannon Diversity Index measured in the sample from the reference subject. . In one embodiment, the Shannon diversity index can be reduced by 1% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 5% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 10% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 15% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 20% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 25% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 30% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 35% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 40% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 45% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 50% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 55% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 60% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 65% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 70% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 75% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 80% compared to Shannon Diversity Index in the sample from thereference subject. In one embodiment, the Shannon Diversity Index can be reduced by 85% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 90% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 95% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 100% compared to Shannon Diversity Index in the sample from the reference subject.

[0098] In some aspects, the beta microbial diversity in the subject is increased compared to beta microbial diversity in the reference subject. For example, beta microbial diversity in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 0.5 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 1.5 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 3 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 5 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 10 times greater than the beta microbial diversity in a sample from a reference subject.

[0099] In one aspect, the relative abundance of the SCFA producing microbe in the subject is increased compared to the relative abundance of the SCFA producing microbe in the reference subject. For example, the relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increase by at least 0.5 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbes in a sample from the subject may be increased by at least 3 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 5 times greater thanthe relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject.

[0100] In some aspects, the number of the SCFA producing microbe in the sample from the subject is decreased compared to number of the SCFA producing microbes in a sample from the reference subject. For example, the number of the SCFA producing microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the number of the SCFA producing microbe in a sample from a reference subject. Number of the SCFA producing microbes in a sample from the subject may be increase by at least 0.5 times greater than the number of the SCFA producing microbe in a sample from a reference subject. Number of the SCFA producing microbe in a sample from the subject may be increased by at least 1.5 times greater than the number of the SCFA producing microbe in a sample from a reference subject. Number of the SCFA producing microbes in a sample from the subject may be increased by at least 3 times greater than the number of the SCFA producing microbes in a sample from a reference subject. Number of the SCFA producing microbe in a sample from the subject may be increased by at least 5 times greater than the number of the SCFA producing microbe in a sample from a reference subject. The number of the SCFA producing microbes in a sample from the subject may be increased by at least 10 times greater than the number of the SCFA producing microbes in a sample from a reference subject.

[0101] In some aspects, the SCFA producing microbe includes faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, anaerostipes, dialister, flavonifractior, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

[0102] In one aspect, the SCFA producing microbe includes faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

[0103] In one aspect, the relative abundance of the gas producing microbe in the subject is increased compared to the relative abundance of the gas producing microbe in the reference subject. For example, the relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 0.5 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject.Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 3 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 5 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbes in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject.

[0104] In some aspects, the gas producing microbe includes bacteroides fragilis, escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, methanobrevibacter oralis, or a combination thereof. In one aspect, the gas producing microbe includes escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, or a combination thereof.

[0105] In one aspect, the relative abundance of the microbe associated metabolic pathway in the subject is increased compared to the relative abundance of the microbe associated metabolic pathway in the sample from the reference subject. For example, the relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundance of the metabolic pathway microbe in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 0.5 times greater than the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 3 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 5 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject.

[0106] In some aspects, the metabolic pathway is methanogenesis from H2 and CO2; methanogenesis from acetate; assimilatory sulfate reduction I; superpathway of sulfate assimilation and cysteine biosynthesis; L-lysine biosynthesis; preQO biosynthesis, pyrimidine deoxyribonucleosides salvage; superpathway of polyamine biosynthesis I; CMP-3-3deoxy-D- manno-octulosonate biosynthesis, incomplete reductive TCA cycle; pyrimidine deoxyribonucleotide phosphorylation; superpathway of pyrimidine ribonucleotides de novo biosynthesis; superpathway of guanosine nucleotides de novo biosynthesis I; hexitol fermentation to lactate, formate, ethanol, and acetate; glycogen biosynthesis I (from ADP-D-Glucose); or a combination thereof. In one aspect, the pathway is pyrimidine deoxyribonucleotide phosphorylation.

[0107] In one aspect, the relative abundance of the pathogenic microbe in the subject is increased compared to the relative abundance of the pathogenic microbe in the reference subject. For example, the relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 0.5 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 3 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 5 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject.

[0108] In some aspects, the number of the pathogenic microbes in the sample from the subject is increased compared to number of the pathogenic microbe in a sample from the reference subject. For example, the number of pathogenic microbes in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the number of the pathogenic microbe in a sample from a reference subject. The number of the pathogenic microbes in a sample from the subject may be increased by at least 0.5 times greater than the number of the pathogenic microbe in a sample from a reference subject. The number of the pathogenic microbes in a sample from thesubject may be increased by at least 1.5 times greater than the number of the pathogenic microbe in a sample from a reference subject. Number of the pathogenic microbe in a sample from the subject may be increased by at least 3 times greater than the number of the pathogenic microbe in a sample from a reference subject. The number of pathogenic microbes in a sample from the subject may be increased by at least 5 times greater than the number of the pathogenic microbes in a sample from a reference subject. The number of the pathogenic microbes in a sample from the subject may be increased by at least 10 times greater than the number of the pathogenic microbe in a sample from a reference subject.

[0109] In some aspects, the pathogenic microbe includes klebsiella, enterobacter, shigella, salmonella, citrobacter, serratia, proteus, or a combination thereof. In one aspect, the pathogenic microbe is klebsiella, shigella, salmonella, or a combination thereof.

[0110] In some aspects, the reference subject includes a healthy subject or the subject at an earlier time point.

[0111] In some aspects, the sample includes a fecal sample, a mucosal, sample, a rectal swab, an intestinal fluid sample, or a combination there of. In one aspect, the sample includes a fecal sample.

[0112] In some aspects, the microbial modulator includes a probiotic, a prebiotic, a special diet, a supplement, a functional food, an SCFA production modulator, a gut homeostasis modulator, a GLP-1 hormone secretion modulator, or a combination thereof. In one aspect, the probiotic is a custom probiotic.

[0113] In some aspects, the diet includes a high fiber diet, a high potassium diet, a vegetablerich diet, a fruit-rich diet, a carbohydrate-rich diet, or a combination thereof. In one aspect, the high potassium diet includes a banana, an apricot, a peach, or a combination thereof. In one aspect, the vegetable-rich diet includes a lettuce, a tomato, a zucchini, an okra, or a combination thereof. In one aspect, the fruit-rich diet includes a cantaloupe, a grape, a berry, a cherry, an avocado, an olive, or a combination thereof. In one aspect, the carbohydrate-rich diet includes gluten-free bread, rice bread, rice, or a combination thereof. In one aspect, the supplement includes bifidobacterium breve SG05, lactobacillus rhamnosus SGI 6, lactococcus lactis SGI 4, bifidobacterium bifidum SG28, flaxseed powder, turmeric, bifidobacterium infantis SG25, limosilactobacillius reuteri SG01, lactobacillus paracasei SGI 7, bifidobacterium longum SGO, lactobacillus delbrueckii subsp. bulgaricus SG10, lactobacillus plantarum SGO6, bifidobacterium breve SG05, lactobacillus rhamnosus SG16, lactobacillus rhamnosus SG21, bifidobacterium bifidum SG28, or a combination thereof.

[0114] In some aspects, the metabolic disorder includes diabetes, obesity, phenylketonuria (PKU), Gaucher’s disease, hemochromatosis, mitochondrial disorders, hyperthyroidism, hypothyroidism, Wilson’s disease, maple syrup urine disease (MSUD), galactosemia, or a combination thereof.

[0115] In one aspect, the metabolic disorder includes diabetes, obesity, or a combination thereof.

[0116] In one embodiment, the present disclosure provides a method of determining a predisposition to or diagnosing a metabolic disorder in a subject including: detecting a microbial composition of a gut microbiome in a sample from the subject; detecting a difference in the microbial composition of the subject compared to a reference subject, wherein the difference in the microbial composition of the subject compared to the reference subject is indicative of predisposition to or presence of the metabolic disorder; thereby determining a predisposition to or diagnosing the metabolic disorder in the subject.

[0117] In some aspects, detecting the microbial composition includes sequencing microbial DNA from the sample from the subject. Examples of sequencing may include but are not limited to sanger sequencing, maxam-gilbert sequencing, next-generation sequencing (NGS), pyrosequencing, targeted sequencing, RNA sequencing (RNA-Seq), bisulfite sequencing, metagenomic sequencing, de novo sequencing, exome sequencing, ChIP sequencing (ChlP-Seq), mate pair sequencing, paired-end sequencing, epigenomic sequencing, long read sequencing, cycle sequencing, RAD-Seq (restriction site-associated DNA sequencing), amplicon sequencing, shotgun sequencing, tilling sequencing, 3D sequencing, 4D sequencing, capture sequencing, CRISPR sequencing, whole-genome sequencing (WGS), microRNA sequencing, expression sequencing, MeDIP-Seq, RRB-sequencing, dP-Seq, sequencing for functional genomics, ATAC- Seq, pooled library sequencing, shallow sequencing, CAGE-Seq, Single-Cell Sequencing, CLIP- Seq, high-throughput sequencing, SOLiD sequencing, SMRT sequencing, MPSS, polony sequencing, solexa sequencing, ion torrent semi-conductor sequencing, DNA nanoball sequencing, sequencing by hybridization, and nanopore sequencing. In one aspect, the sequencing microbial DNA includes whole genome sequencing.

[0118] In some aspects, detecting microbiome diversity includes detecting alpha microbial diversity, beta microbial diversity, or a combination thereof.In one aspect, the alpha microbial diversity in the sample from the subject is reduced compared to alpha microbial diversity in a sample from the reference subject. For example, alpha microbial diversity in the sample from the subject is reduced or decreased compared to alpha microbial diversity in a sample from the reference subject. The reduction includes any reduction of the alphamicrobial diversity (e.g., 1% reduction of the alpha microbial diversity), up to a complete reduction of the alpha microbial diversity (e.g., a 100% reduction of the alpha microbial diversity). The alpha microbial diversity can be reduced or decreased by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 05, 96, 97, 98, 99 or 100% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 1% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 5% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 10% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 15% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 20% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 25% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 30% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 35% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 40% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 45% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 50% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 55% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 60% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 65% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 70% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 75% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 80% compared to alpha microbial diversity in the sample from the reference subject. In oneembodiment, the alpha microbial diversity can be reduced by 85% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 90% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 95% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the alpha microbial diversity can be reduced by 100% compared to alpha microbial diversity in the sample from the reference subject.

[0119] In one aspect detecting the alpha microbial diversity includes using the Shannon Diversity Index. For example, the Shannon Diversity Index measured in the sample from the subject is reduced or decreased compared to Shannon Diversity Index measured in a sample from the reference subject. The reduction includes any reduction of the Shannon Diversity Index (e.g., 1% reduction of the Shannon Diversity Index), up to a complete reduction of the Shannon Diversity Index (e.g., a 100% reduction of the Shannon Diversity Index). The Shannon Diversity Index can be reduced or decreased by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 05, 96, 97, 98, 99 or 100% compared to Shannon Diversity Index measured in the sample from the reference subject. . In one embodiment, the Shannon Diversity Index can be reduced by 1% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 5% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 10% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 15% compared to the Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 20% compared to alpha microbial diversity in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 25% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 30% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 35% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 40% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 45% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 50% compared to Shannon Diversity Index in the sample from the reference subject.In one embodiment, the Shannon Diversity Index is reduced by 55% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 60% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 65% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index reduced by 70% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 75% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 80% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index can be reduced by 85% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 90% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 95% compared to Shannon Diversity Index in the sample from the reference subject. In one embodiment, the Shannon Diversity Index is reduced by 100% compared to Shannon Diversity Index in the sample from the reference subject.

[0120] In some aspects, the beta microbial diversity in the subject is increased compared to beta microbial diversity in the reference subject. For example, beta microbial diversity in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 0.5 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 1.5 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 3 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 5 times greater than the beta microbial diversity in a sample from a reference subject. Beta microbial diversity in a sample from the subject may be increased by at least 10 times greater than the beta microbial diversity in a sample from a reference subject.

[0121] In one aspect, the relative abundance of the SCFA producing microbe in the subject is increased compared to the relative abundance of the SCFA producing microbe in the reference subject. For example, the relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundanceof the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increase by at least 0.5 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbes in a sample from the subject may be increased by at least 3 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 5 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject. Relative abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the SCFA producing microbe in a sample from a reference subject.

[0122] In some aspects, the number of the SCFA producing microbe in the sample from the subject is decreased compared to number of the SCFA producing microbes in a sample from the reference subject. For example, the number of the SCFA producing microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the number of the SCFA producing microbe in a sample from a reference subject. Number of the SCFA producing microbes in a sample from the subject may be increase by at least 0.5 times greater than the number of the SCFA producing microbe in a sample from a reference subject. Number abundance of the SCFA producing microbe in a sample from the subject may be increased by at least 1.5 times greater than the number of the SCFA producing microbe in a sample from a reference subject. Number of the SCFA producing microbes in a sample from the subject may be increased by at least 3 times greater than the number of the SCFA producing microbes in a sample from a reference subject. Number of the SCFA producing microbe in a sample from the subject may be increased by at least 5 times greater than the number of the SCFA producing microbe in a sample from a reference subject. The number of the SCFA producing microbes in a sample from the subject may be increased by at least 10 times greater than the number of the SCFA producing microbes in a sample from a reference subject.

[0123] In some aspects, the SCFA producing microbe includes faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, anaerostipes, dialister, flavonifractior, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

[0124] In one aspect, the SCFA producing microbe includes faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

[0125] In one aspect, the relative abundance of the gas producing microbe in the subject is increased compared to the relative abundance of the gas producing microbe in the reference subject. For example, the relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 0.5 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 3 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbe in a sample from the subject may be increased by at least 5 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject. Relative abundance of the gas producing microbes in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the gas producing microbe in a sample from a reference subject.

[0126] In some aspects, the gas producing microbe includes bacteroides fragilis, escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, methanobrevibacter oralis, or a combination thereof. In one aspect, the gas producing microbe includes escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, or a combination thereof.

[0127] In one aspect, the relative abundance of the microbe associated metabolic pathway in the subject is increased compared to the relative abundance of the microbe associated metabolic pathway in the sample from the reference subject. For example, the relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundance of the metabolic pathway microbe in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may beincreased by at least 0.5 times greater than the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 3 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 5 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject. Relative abundance of the metabolic pathway in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the metabolic pathway in a sample from a reference subject.

[0128] In some aspects, the metabolic pathway is methanogenesis from H2 and CO2; methanogenesis from acetate; assimilatory sulfate reduction I; superpathway of sulfate assimilation and cysteine biosynthesis; L-lysine biosynthesis; preQO biosynthesis, pyrimidine deoxyribonucleosides salvage; superpathway of polyamine biosynthesis I; CMP-3-3deoxy-D- manno-octulosonate biosynthesis, incomplete reductive TCA cycle; pyrimidine deoxyribonucleotide phosphorylation; superpathway of pyrimidine ribonucleotides de novo biosynthesis; superpathway of guanosine nucleotides de novo biosynthesis I; hexitol fermentation to lactate, formate, ethanol, and acetate; glycogen biosynthesis I (from ADP-D-Glucose); or a combination thereof. In one aspect, the pathway is pyrimidine deoxyribonucleotide phosphorylation.

[0129] In one aspect, the relative abundance of the pathogenic microbe in the subject is increased compared to the relative abundance of the pathogenic microbe in the reference subject. For example, the relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 0.5 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 1.5 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 3 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 5 times greater than the relative abundance of the pathogenic microbe ina sample from a reference subject. Relative abundance of the pathogenic microbe in a sample from the subject may be increased by at least 10 times greater than the relative abundance of the pathogenic microbe in a sample from a reference subject.

[0130] In some aspects, the number of the pathogenic microbes in the sample from the subject is increased compared to number of the pathogenic microbe in a sample from the reference subject. For example, the number of pathogenic microbes in a sample from the subject may be increased by at least 0.5 times to 10 times greater than the number of the pathogenic microbe in a sample from a reference subject. The number of the pathogenic microbes in a sample from the subject may be increased by at least 0.5 times greater than the number of the pathogenic microbe in a sample from a reference subject. The number of the pathogenic microbes in a sample from the subject may be increased by at least 1.5 times greater than the number of the pathogenic microbe in a sample from a reference subject. Number of the pathogenic microbe in a sample from the subject may be increased by at least 3 times greater than the number of the pathogenic microbe in a sample from a reference subject. The number of pathogenic microbes in a sample from the subject may be increased by at least 5 times greater than the number of the pathogenic microbes in a sample from a reference subject. The number of the pathogenic microbes in a sample from the subject may be increased by at least 10 times greater than the number of the pathogenic microbe in a sample from a reference subject.

[0131] In some aspects, the pathogenic microbe includes klebsiella, enterobacter, shigella, salmonella, citrobacter, serratia, proteus, or a combination thereof. In one aspect, the pathogenic microbe is klebsiella, shigella, salmonella, or a combination thereof.

[0132] In some aspects, the reference subject includes a healthy subject or the subject at an earlier time point.

[0133] In some aspects, the sample includes a fecal sample, a mucosal, sample, a rectal swab, an intestinal fluid sample, or a combination there of. In one aspect, the sample includes a fecal sample.

[0134] In some aspects, the metabolic disorder includes diabetes, obesity, phenylketonuria (PKU), Gaucher’s disease, hemochromatosis, mitochondrial disorders, hyperthyroidism, hypothyroidism, Wilson’s disease, maple syrup urine disease (MSUD), galactosemia, or a combination thereof.

[0135] In one aspect, the metabolic disorder includes diabetes, obesity, or a combination thereof.

[0136] Presented below are examples discussing changes in the microbial composition of the gut in obesity contemplated for the discussed applications. The following examples are providedto further illustrate the embodiments of the present invention but are not intended to limit the scope of the invention. While they are typical of those that might be used, other procedures, methodologies, or techniques known to those skilled in the art may alternatively be used.EXAMPLES

[0137] The following examples are provided to further illustrate the embodiments of the present invention but are not intended to limit the scope of the invention. While they are typical of those that might be used, other procedures, methodologies, or techniques known to those skilled in the art may alternatively be used.EXAMPLE 1Methods

[0138] The microbiome of the gut was evaluated using GI SereniT™ and Whole Genome Sequencing. The criteria used to select the study cohorts are described in Table 1.

[0139] Table 1: Criteria for cohort selection

[0140] Alpha diversity of the gut microbiome was evaluated in a healthy and obesity cohort.EXAMPLE 2Gut Microbiome Diversity in Obesity and Healthy Cohort

[0141] Differences in gut microbial composition and metabolic efficiency may be responsible for an individual’s predisposition to metabolic disorders such as obesity and diabetes. Alpha diversity in the obesity cohort is significantly different from health cohort with lower species diversity (FIG. 2 and Table 2).

[0142] Table 2: Alpha diversity from health and obesity cohorts

[0143] Beta diversity of the gut microbiota composition is significantly different from healthy and obesity cohorts (FIG. 3 and Table 3).

[0144] Table 3: Beta diversity from health and obesity cohortsEXAMPLE 3SCFA producing Microbes in Obesity and Healthy Cohort

[0145] SCFA producing microbes of the gut decreases in the obesity cohort compared to SCFA producing microbes of the gut in the healthy cohort (FIG. 4 and Table 4).

[0146] Table 4: SCFAEXAMPLE 4Gas Producing Microbes in Obesity and Healthy Cohort

[0147] Gas producing microbes of the gut are increased in the obesity cohort compared to gas producing microbes of the gut in the healthy cohort (FIG. 5 and Table 5). The obesity cohort also showed a higher abundance of pyrimidine deoxyribonucleotide phosphorylation compared to the healthy cohort (FIG. 6).

[0148] Table 5: Gas productionEXAMPLE 5Pathogenic Microbes in Obesity and Healthy Cohort

[0149] Pathogenic microbes of the gut are increased in the obesity cohort compared to pathogenic microbes of the gut in the healthy cohort (FIG. 7 and Table 6). The importance of certain microbes for making accurate predictions are shown in FIG. 8. Fibers are important in regulating the metabolic health pathways associated with Obesity (FIG. 9). Prebiotics and probiotics supplementation can help re-establish the homeostasis of the Gut (Table 6 and Table 7).

[0150] Table 6: Pathogens

[0151] Table 7: Protocols for the 3 Microbiome Signatures Impacting Metabolic Health.

[0152] Although the invention has been described with reference to the presently preferred embodiment, it should be understood that various modifications can be made without departing from the spirit of the invention. Accordingly, the invention is limited only by the following claims.

Claims

WHAT IS CLAIMED IS:

1. A method of treating a metabolic disorder in a subject comprising: a) detecting a microbial composition of a gut microbiome in a sample from the subject; b) detecting a difference in the microbial composition of the subject compared to a reference subject; and c) administering to the subject a microbial modulator; thereby treating the metabolic disorder in the subject.

2. The method of claim 1, wherein detecting the microbial composition comprises detecting microbiome diversity, a short-chain fatty acids (SCFAs) producing microbe, a gas producing microbe, a metabolic pathway associated microbe, a pathogenic microbe, or a combination thereof.

3. The method of claim 1, wherein detecting the microbial composition comprises sequencing microbial DNA from the sample from the subject.

4. The method of claim 3, wherein the sequencing the microbial DNA comprises whole genome sequencing.

5. The method of claim 2, wherein detecting microbiome diversity comprises detecting alpha microbial diversity, beta microbial diversity, microbe associated metabolic pathway, or a combination thereof.

6. The method of claim 5, wherein the alpha microbial diversity in the sample from the subject is reduced compared alpha microbial diversity in a sample from the reference subject.

7. The method of claim 5 or 6, wherein detecting the alpha microbial diversity comprises using Shannon Diversity Index.

8. The method of claim 6, wherein the beta microbial diversity in the subject is increased compared beta microbial diversity in the reference subject.

9. The method of claim 2, wherein relative abundance of the SCFA producing microbe in the subject is increased compared to relative abundance of the SCFA producing microbe in the reference subject.

10. The method of claim 2, wherein number of the SCFA producing microbe in the sample from the subject is decreased compared to number of the SCFA producing microbe in a sample from the reference subject.

11. The method of claim 9, wherein the SCFA producing microbe comprises faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, anaerostipes, dialister, flavonifractior, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

12. The method of claim 11, wherein the SCFA producing microbe comprises faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

13. The method of claim 2, wherein relative abundance of the gas producing microbe in the subject is increased compared to the relative abundance of the gas producing microbe in the reference subject.

14. The method of claim 13, wherein the gas producing microbe comprises bacteroides fragilis, escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, methanobrevibacter oralis, or a combination thereof.

15. The method of claim 14, wherein the gas producing microbe comprises escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, or a combination thereof.

16. The method of claim 5, wherein the relative abundance of microbe associated metabolic pathway in the subject is increased compared to the relative abundance of the microbe associated metabolic pathway in the sample from the reference subject.

17. The method of claim 16, wherein the metabolic pathway is methanogenesis from H2 and CO2; methanogenesis from acetate; assimilatory sulfate reduction I; superpathway of sulfate assimilation and cysteine biosynthesis; L-lysine biosynthesis; preQO biosynthesis, pyrimidine deoxyribonucleosides salvage; superpathway of polyamine biosynthesis I; CMP-3-3deoxy-D-manno-octulosonate biosynthesis, incomplete reductive TCA cycle; pyrimidine deoxyribonucleotide phosphorylation; superpathway of pyrimidine ribonucleotides de novo biosynthesis; superpathway of guanosine nucleotides de novo biosynthesis I; hexitol fermentation to lactate, formate, ethanol, and acetate; glycogen biosynthesis I (from ADP-D-Glucose); or a combination thereof.

18. The method of claim 17, wherein the metabolic pathway is pyrimidine deoxyribonucleotide phosphorylation.

19. The method of claim 2, wherein the relative abundance of the pathogenic microbe in the subject is increased compared to the relative abundance of the pathogenic microbe in the reference subject.

20. The method of claim 2, wherein a number of the pathogenic microbe in the sample from the subject is increased compared to a number of the pathogenic microbe in a sample from the reference subject.

21. The method of claim 19 or 20, wherein the pathogenic microbe comprises klebsiella, enterobacter, shigella, salmonella, citrobacter, serratia, proteus, or a combination thereof.

22. The method of claim 21, wherein the pathogenic microbe comprises klebsiella, shigella, salmonella, or a combination thereof.

23. The method of any of claims 1 to 22, wherein the reference subject is a healthy subject or the subject at an earlier time point.

24. The method of any of claims 1 to 23, wherein the sample comprises a fecal sample, a mucosal, sample, a rectal swab, an intestinal fluid sample, or a combination there of.

25. The method of claims 24, wherein the sample comprises a fecal sample.

26. The method of any of claims 1 to 25, wherein the microbial modulator comprises a probiotic, a prebiotic, a special diet, a supplement, a functional food, an SCFA production modulator, a gut homeostasis modulator, a GLP-1 hormone secretion modulator, or a combination thereof.

27. The method of claim 26, wherein the probiotic is a combination probiotic.

28. The method of claim 26, wherein the special diet comprises a high fiber diet, a high potassium diet, a vegetable -rich diet, a fruit-rich diet, a carbohydrate-rich diet, or a combination thereof.

29. The method of claim 28, wherein the high potassium diet comprises a banana, a apricot, a peach, or a combination thereof.

30. The method of claim 28, wherein the vegetable-rich diet comprises a lettuce, a tomato, a zucchini, an okra, or a combination thereof.

31. The method of claim 28, wherein the fruit-rich diet comprises a cantaloupe, a grape, a berry, a cherry, an avocado, an olive, or a combination thereof.

32. The method of claim 28, wherein the low or high carbohydrate diet comprises gluten- free bread, rice bread, rice, or a combination thereof.

33. The method of claim 26, wherein the supplement comprises bifidobacterium breve SG05, lactobacillus rhamnosus SG16, lactococcus lactis SG14, bifidobacterium bifidumSG28, flaxseed powder, turmeric, bifidobacterium infantis SG25, limosilactobacillius reuteri SG01, lactobacillus paracasei SGI 7, bifidobacterium longum SGO, lactobacillus delbrueckii subsp. bulgaricus SG10, lactobacillus plantarum SGO6, bifidobacterium breve SG05, lactobacillus rhamnosus SGI 6, lactobacillus rhamnosus SG21, bifidobacterium bifidum SG28, or a combination thereof.

34. The method of claim 1, wherein the metabolic disorder comprises diabetes, obesity, phenylketonuria (PKU), Gaucher’s disease, hemochromatosis, mitochondrial disorders, hyperthyroidism, hypothyroidism, Wilson’s disease, maple syrup urine disease (MSUD), galactosemia, or a combination thereof.

35. A method of stratifying subjects for administration of a microbial modulator comprising: a) detecting a microbial composition of a gut microbiome in a sample from the subject; b) detecting a difference in the microbial composition of the subject compared to a reference subject; c) stratifying the subject based on the difference in the microbial composition; and d) administering a microbial modulator to the subject based on the stratification in (c).

36. The method of claim 35, wherein detecting the microbial composition comprises detecting microbiome diversity, a short-chain fatty acids (SCFAs) producing microbe, a gas producing microbe, a metabolic pathway associated microbe, a pathogenic microbe, or a combination thereof.

37. The method of claim 35, wherein detecting the microbial composition comprises sequencing microbial DNA from the sample from the subject.

38. The method of claim 37, wherein the sequencing the microbial DNA comprises whole genome sequencing.

39. The method of claim 36, wherein detecting microbiome diversity comprises detecting alpha microbial diversity, beta microbial diversity, a microbe associated metabolic pathway, or a combination thereof.

40. The method of claim 39, wherein the alpha microbial diversity in the sample from the subject is reduced compared to the alpha microbial diversity in a sample from the reference subject.

41. The method of claim 39 or 40, wherein detecting the alpha microbial diversity comprises using Shannon Diversity Index.

42. The method of claim 39, wherein the beta microbial diversity in the subject is increased compared beta microbial diversity in the reference subject.

43. The method of claim 36, wherein relative abundance of the SCFA producing microbe in the subject is increased compared to relative abundance of the SCFA producing microbe in the reference subject.

44. The method of claim 36, wherein number of the SCFA producing microbe in the sample from the subject is decreased compared to number of the SCFA producing microbe in a sample from the reference subject.

45. The method of claim 43 or 44, wherein the SCFA producing microbe comprises faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, anaerostipes, dialister, flavonifractior, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

46. The method of claim 45, wherein the SCFA producing microbe comprises faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

47. The method of claim 36, wherein relative abundance of the gas producing microbe in the subject is increased compared to the relative abundance of the gas producing microbe in the reference subject.

48. The method of claim 47, wherein the gas producing microbe comprises bacteroides fragilis, escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, methanobrevibacter oralis, or a combination thereof.

49. The method of claim 48, wherein the gas producing microbe comprises escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, or a combination thereof.

50. The method of claim 39, wherein relative abundance of the metabolic pathway in the subject is increased compared to relative abundance of the metabolic pathway in the sample from the reference subject.

51. The method of claim 50, wherein the metabolic pathway is methanogenesis from H2 and CO2; methanogenesis from acetate; assimilatory sulfate reduction I; superpathway of sulfate assimilation and cysteine biosynthesis; L-lysine biosynthesis; preQO biosynthesis,pyrimidine deoxyribonucleosides salvage; superpathway of polyamine biosynthesis I; CMP-3-3deoxy-D-manno-octulosonate biosynthesis, incomplete reductive TCA cycle; pyrimidine deoxyribonucleotide phosphorylation; superpathway of pyrimidine ribonucleotides de novo biosynthesis; superpathway of guanosine nucleotides de novo biosynthesis I; hexitol fermentation to lactate, formate, ethanol, and acetate; glycogen biosynthesis I (from ADP-D-Glucose); or a combination thereof.

52. The method of claim 51, wherein the metabolic pathway is pyrimidine deoxyribonucleotide phosphorylation.

53. The method of claim 36, wherein the relative abundance of the pathogenic microbe in the subject is increased compared to the relative abundance of the pathogenic microbe in the reference subject.

54. The method of claim 36, wherein a number of the pathogenic microbes in the sample from the subject is increased compared to a number of the pathogenic microbes in a sample from the reference subject.

55. The method of claim 53 or 54, wherein the pathogenic microbe comprises klebsiella, enterobacter, shigella, salmonella, citrobacter, serratia, proteus, or a combination thereof.

56. The method of claim 55, wherein the pathogenic microbe comprises klebsiella, shigella, salmonella, or a combination thereof.

57. The method of any of claims 35 to 56, wherein the reference subject is a healthy subject or the subject at an earlier time point.

58. The method of any of claims 35 to 57, wherein the sample comprises a fecal sample, a mucosal, sample, a rectal swab, an intestinal fluid sample, or a combination there of.

59. The method of claims 58, wherein the sample comprises a fecal sample.

60. The method of any of claims 35 to 59, wherein the microbial modulator comprises a probiotic, a prebiotic, a special diet, a supplement, a functional food, an SCFA production modulator, a gut homeostasis modulator, a GLP-1 hormone secretion modulator, or a combination thereof.

61. The method of claim 60, wherein the probiotic is a combination probiotic.

62. The method of claim 60, wherein the special diet comprises a high fiber diet, a high potassium diet, a vegetable -rich diet, a fruit-rich diet, a carbohydrate-rich diet, or a combination thereof.

63. The method of claim 62, wherein the high potassium diet comprises a banana, a apricot, a peach, or a combination thereof.

64. The method of claim 62, wherein the vegetable-rich diet comprises a lettuce, a tomato, a zucchini, an okra, or a combination thereof.

65. The method of claim 62, wherein the fruit-rich diet comprises a cantaloupe, a grape, a berry, a cherry, an avocado, an olive, or a combination thereof.

66. The method of claim 62, wherein the low or high carbohydrate diet comprises gluten- free bread, rice bread, rice, or a combination thereof.

67. The method of claim 60, wherein the supplement comprises bifidobacterium breve SG05, lactobacillus rhamnosus SG16, lactococcus lactis SG14, bifidobacterium bifidum SG28, flaxseed powder, turmeric, bifidobacterium infantis SG25, limosilactobacillius reuteri SG01, lactobacillus paracasei SGI 7, bifidobacterium longum SGO, lactobacillus delbrueckii subsp. bulgaricus SG10, lactobacillus plantarum SGO6, bifidobacterium breve SG05, lactobacillus rhamnosus SGI 6, lactobacillus rhamnosus SG21, bifidobacterium bifidum SG28, or a combination thereof.

68. The method of claim 35, wherein the metabolic disorder comprises diabetes, obesity, phenylketonuria (PKU), Gaucher’s disease, hemochromatosis, mitochondrial disorders, hyperthyroidism, hypothyroidism, Wilson’s disease, maple syrup urine disease (MSUD), galactosemia, or a combination thereof.

69. The method of claim 68, wherein the metabolic disorder comprises diabetes, obesity, or a combination thereof.

70. A method of determining a predisposition to or diagnosing a metabolic disorder in a subject comprising: a) detecting a microbial composition of a gut microbiome in a sample from the subject; and b) detecting a difference in the microbial composition of the subject compared to a reference subject, wherein the difference in the microbial composition of the subject compared to the reference subject is indicative of predisposition to or presence of the metabolic disorder; thereby determining a predisposition to or diagnosing the metabolic disorder in the subject.

71. The method of claim 70, wherein detecting the microbial composition comprises detecting microbiome diversity, a short-chain fatty acids (SCFAs) producing microbe, a gas producing microbe, a microbe associated metabolic pathway, a pathogenic microbe, or a combination thereof.

72. The method of claim 70, wherein detecting the microbial composition comprises sequencing microbial DNA from the sample from the subject.

73. The method of claim 72, wherein the sequencing the microbial DNA comprises whole genome sequencing.

74. The method of claim 71, wherein detecting microbiome diversity comprises detecting alpha microbial diversity, beta microbial diversity, or a combination thereof.

75. The method of claim 74, wherein the alpha microbial diversity in the sample from the subject is reduced compared alpha microbial diversity in a sample from the reference subject.

76. The method of claim 74 or 75, wherein detecting the alpha microbial diversity comprises using Shannon Diversity Index.

77. The method of claim 74, wherein the beta microbial diversity in the subject is increased compared beta microbial diversity in the reference subject.

78. The method of claim 71, wherein relative abundance of the SCFA producing microbe in the subject is increased compared to relative abundance of the SCFA producing microbe in the reference subject.

79. The method of claim 71, wherein number of the SCFA producing microbe in the sample from the subject is decreased compared to number of the SCFA producing microbe in a sample from the reference subject.

80. The method of claim 78 or 79, wherein the SCFA producing microbe comprises faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, anaerostipes, dialister, flavonifractior, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

81. The method of claim 80, wherein the SCFA producing microbe comprises faecalibacterium, roseburia, eubacterium, ruminococcus, bifidobacterium, coprococcus, odoribacter, lactobacillus, butyricimonas, butyrivibrio, butyricicoccus, or a combination thereof.

82. The method of claim 71, wherein relative abundance of the gas producing microbe in the subject is increased compared to the relative abundance of the gas producing microbe in the reference subject.

83. The method of claim 82, wherein the gas producing microbe comprises bacteroides fragilis, escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum,methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, methanobrevibacter oralis, or a combination thereof.

84. The method of claim 83, wherein the gas producing microbe comprises escherichia coli, akkermanksia muciniphila, bifidobacterium pseudocatenulatum, methanobrevibacter smithii, deslfovibrio desulfuricans, lactobacillus casei, helicobacter pylori, methanosphaera stadtmanae, or a combination thereof.

85. The method of claim 74, wherein relative abundance of the metabolic pathway in the subject is increased compared to relative abundance of the metabolic pathway in the sample from the reference subject.

86. The method of claim 85, wherein the metabolic pathway is methanogenesis from H2 and CO2; methanogenesis from acetate; assimilatory sulfate reduction I; superpathway of sulfate assimilation and cysteine biosynthesis; L-lysine biosynthesis; preQO biosynthesis, pyrimidine deoxyribonucleosides salvage; superpathway of polyamine biosynthesis I; CMP-3-3deoxy-D-manno-octulosonate biosynthesis, incomplete reductive TCA cycle; pyrimidine deoxyribonucleotide phosphorylation; superpathway of pyrimidine ribonucleotides de novo biosynthesis; superpathway of guanosine nucleotides de novo biosynthesis I; hexitol fermentation to lactate, formate, ethanol, and acetate; glycogen biosynthesis I (from ADP-D-Glucose); or a combination thereof.

87. The method of claim 86, wherein the metabolic pathway is pyrimidine deoxyribonucleotide phosphorylation.

88. The method of claim 71, wherein the relative abundance of the pathogenic microbe in the subject is increased compared to the relative abundance of the pathogenic microbe in the reference subject.

89. The method of claim 71, wherein a number of the pathogenic microbes in the sample from the subject is increased compared to a number of the pathogenic microbes in a sample from the reference subject.

90. The method of claim 88 or 89, wherein the pathogenic microbe comprises klebsiella, enterobacter, shigella, salmonella, citrobacter, serratia, proteus, or a combination thereof.

91. The method of claim 90, wherein the pathogenic microbe comprises klebsiella, shigella, salmonella, or a combination thereof.

92. The method of any of claims 70 to 91, wherein the reference subject is a healthy subject or the subject at an earlier time point.

93. The method of any of claims 70 to 92, wherein the sample comprises a fecal sample, a mucosal, sample, a rectal swab, an intestinal fluid sample, or a combination there of.

94. The method of claims 93, wherein the sample comprises a fecal sample.

95. The method of any of claims 70 to 94, wherein the metabolic disorder is diabetes, obesity, phenylketonuria (PKU), Gaucher’s disease, hemochromatosis, mitochondrial disorders, hyperthyroidism, hypothyroidism, Wilson’s disease, maple syrup urine disease (MSUD), galactosemia, or a combination thereof.

96. The method of claim 95, wherein the metabolic disorder comprises obesity, diabetes, or a combination thereof.

97. The method of any of claims 70 to 96, wherein the reference subject is a healthy subject or the subject at an earlier time point.

Images