DEVICES AND SYSTEMS FOR THE DETECTION AND MANIPULATION OF THE GASTROINTESTINAL MICROBIOM

Description

RELATED APPLICATIONS

[0001] This application claims the benefit of U.S. Provisional Application Nos. 62 / 679,659, filed June 1, 2018; 62 / 751,209, filed October 26, 2018; and 62 / 829,225, filed April 4, 2019.TECHNICAL FIELD

[0002] The disclosure relates to gastrointestinal (GI) tract microbiome detection and manipulation devices, systems, and methods.BACKGROUND

[0003] The human gastrointestinal (GI) tract is colonized by a diverse and complex microbial community that includes many different microorganisms, particularly diverse species and strains of bacteria and archaea. These organisms form a commensal community that contributes to the health and well-being of the individual. While each individual is inhabited by their own signature microbial community, the diversity of microorganisms forming this community may have an effect on a plethora of diseases including allergy, diabetes, obesity, arthritis, neurological disorders, and gastrointestinal disorders (e.g., inflammatory bowel disease). For example, the microbial community interacts with the host immune system to educate it in order to form the necessary response mechanisms to combat external pathogens. This interaction is also necessary in preventing the development of autoimmune diseases.

[0004] WO 2018 / 106931 Al discloses gastrointestinal tract detection methods, devices and systems. WO 2018 / 112441 Al discloses an ingestible device and associated methods. WO 01 / 11077 A2 discloses methods of diagnosing or treating irritable bowel syndrome and other disorders caused by small intestinal bacterial overgrowth. US 2018 / 015100 Al describes combination products for the treatment of bacterial infections and method of producing or dosing of same. Raza Aun et al. "Oral meropenem for superbugs: challenges and opportunities", Drug Discovery Today, 1 February 2021, describes the challenges and opportunities of oral meropenem for superbugs. Akira Ohno et al. "Antibacterial activity and PK / PD of ceftriaxone against penicillin-resistant Streptococcus pneumoniae and [beta]-lactamase-negative ampicillin-resistant Haemophilus influenzae isolates from patients with community-acquired pneumonia", Journal of Infection and Chemotherapy, 30 October 2007, describes antibacterial activity and PK / PD of ceftriaxone against penicillin-resistant Streptococcus pneumoniae and [beta]-lactamase-negative ampicillin-resistant Haemophilus influenzae isolates from patients with community-acquired pneumonia.

[0005] Marek Majewski et al, "Efficacy of Rifaximin, a Nonabsorbed Oral Antibiotic, in the Treatment of Small Intestinal Bacterial Overgrowth", American Journal of Medical Sciences, 1 May 2007, describes the efficacy of rifaximin, a nonabsorbed oral antibiotic in the treatment of small intestinal bacterial overgrowth.SUMMARY

[0006] The invention is as defined in the appended claims. Hereinafter, the term "embodiment(s)" is to be considered as (an) embodiment(s) of the invention only if it falls within the scope of the claim, otherwise it refers to a mere instance of the disclosure.

[0007] The present disclosure relates to methods, devices, and systems for the detection and analysis of the gastrointestinal (GI) tract microbiome. The methods and devices described herein allow for the regio-specific analysis of analytes (e.g., microorganisms) in the GI tract of a subject that form the complex GI tract microbiota. For example, the devices described herein can directly analyze the microbiome of a subject in vivo, or can be used to obtain a sample from the GI tract which can then be analyzed ex vivo. The ability to obtain samples from specific regions of the GI tract may be particularly advantageous in developing personalized therapies for subjects having a gastrointestinal disorder (GID).

[0008] For example, a subject may present to a clinician with one or more symptoms of a GID. Regio-specific samples may be obtained from the GI tract of the subject using a device described herein. These samples can be analyzed ex vivo to identify and characterize the microorganisms in the sample. Individual microbial isolates obtained from the sample can be subjected to antibiotic resistance / sensitivity tests which can be used to develop customized antimicrobial regimens to treat the subject. The same device or a different device (e.g., any of the devices described herein) may then be used to administer a therapeutically effective amount of the antimicrobial regimen proximate to, proximal to, or directly onto the specific discrete locations of the GI tract from which the sample was obtained, or to monitor the GI tract of the subject.

[0009] In one aspect, this disclosure provides a pharmaceutical formulation for use in a method for treating small intestinal bacterial overgrowth (SIBO) in a subject in need thereof, the method comprising: orally administering an effective amount of the pharmaceutical formulation, which comprises an antimicrobial agent, to the subject, thereby treating SIBO in the subject, wherein the antimicrobial agent is meropenem or ceftriaxone and wherein the pharmaceutical formulation is either: formulated for oral administration as a solid dosage form with an enteric coating; or is administered in an ingestible device and released into the small intestine.

[0010] Subsequent references to methods of treatment by therapy or surgery or in vivo diagnosis methods in this disclosure are to be interpreted as references to a pharmaceutical formulation of the invention for use in those methods.

[0011] In some embodiments of any of the methods described herein, the method includes determining antimicrobial susceptibility of a microorganism within the gastrointestinal (GI) tract of a subject including identifying an antimicrobial agent that inhibits the growth of the microorganism, wherein the microorganism has been obtained from a sample having been removed from a ingestible device that retrieved the sample from the GI tract of the subject.

[0012] In some embodiments of any of the methods described herein, the ingestible device includes a sampling chamber configured to collect the sample from the GI tract of the subject. In some embodiments, the sampling chamber includes the antimicrobial agent (e.g., a composition including one or more antibiotics). In some embodiments of any of the methods described herein, the sampling chamber includes an absorptive material.

[0013] In some embodiments of any of the methods described herein, identifying an antimicrobial agent that inhibits the growth of the microorganism includes quantitating and determining the viability of the microorganism obtained from the sample chamber, wherein reduced viability indicates that the microorganism is susceptible to the antimicrobial agent.

[0014] In some embodiments of any of the methods described herein, identifying an antimicrobial agent that inhibits the growth of the microorganism includes contacting a plurality of microorganisms derived from the microorganism with the antimicrobial agent for a predetermined period of time; and detecting growth of the plurality of microorganisms, wherein reduced growth in the presence of the microbial agent relative to a reference indicates that the microorganism is susceptible to the antimicrobial agent, and wherein non-reduced growth in the presence of the microbial agent relative to the reference indicates that the microorganism is resistant to the antimicrobial agent. In some embodiments, the reference includes a plurality of microorganisms derived from the microorganism incubated in the absence of the antimicrobial agent for the predetermined period of time.

[0015] In some embodiments of any of the methods described herein, the ingestible device includes a microprocessor.

[0016] In some embodiments of any of the methods described herein, the ingestible device includes a housing, and the sample chamber is configured within the housing such that, when the device is in the GI tract of the subject, the sample chamber is in selective fluid communication with the GI tract. In some embodiments, the housing is not biodegradable in the GI tract.

[0017] In some embodiments of any of the methods described herein, the ingestible device retrieved the sample from the mouth, the throat, the esophagus, the stomach, the rectum, the anus, the sphincter, the duodenum, the jejunum, the ileum, the ascending colon, the transverse colon, or the descending colon of the subject.

[0018] In some embodiments of any of the methods described herein, the subject may be a human subject. In some embodiments, the human subject has symptomology of a gastrointestinal disorder. In some embodiments, the human subject is a healthy subject. In some embodiments, the human subject has been diagnosed with a gastrointestinal disorder.

[0019] In some embodiments of any of the methods described herein, the microorganism may be a commensal microorganism or a pathogenic microorganism. The microorganism may be a bacterium, an archaeon, a protozoan, a parasite, a virus, or a fungus.

[0020] In some embodiments of any of the methods described herein, the microorganism may be a bacterium of a genus selected from the group consisting of Acetanaerobacterium, Acetivibrio, Aeromonas, Alicyclobacillus, Alkaliphilus, Anaerofustis, Anaerosporobacter, Anaerostipes, Anaerotruncus, Anoxybacillus, Bacillus, Bacteroides, Blautia, Brachyspira, Brevibacillus, Bryantella, Bulleidia, Butyricicoccus, Butyrivibrio, Campylobacter, Catenibacterium, Chlamydiales, Citrobacter, Clostridiales, Clostridium, Collinsella, Coprobacillus, Coprococcus, Coxiella, Deferribacteres, Desulfitobacterium, Desulfotomaculum, Dorea, Eggerthella, Enterobacter, Enterococcus, Escherichia, Erysipelothrix, Erysipelotrichaceae, Ethanoligenens, Eubacterium, Faecalibacterium, Filifactor, Flavonifractor, Flexistipes, Fulvimonas, Fusobacterium, Gemmiger, Geobacillus, Gloeobacter, Haemophilus, Helicobacter, Holdemania, Hydrogenoanaerobacterium, Klebsiella, Kocuria, Lachnobacterium, Lachnospira, Lactobacillus, Lactonifactor, Leptospira, Lutispora, Lysinibacillus, Mollicutes, Moorella, Nocardia, Oscillibacter, Oscillospira, Paenibacillus, Papillibacter, Plesiomonas, Proteus, Pseudoflavoniftactor, Pseudomonas, Robinsoniella, Roseburia, Ruminococcaceae, Ruminococcus, Saccharomonospora, Sarcina, Salmonella, Solobacterium, Shigella, Sporobacter, Sporolactobacillus, Streptococcus, Streptomyces, Subdoligranulum, Sutterella, Staphylococcus, Syntrophococcus, Thermoanaerobacter, Thermobifida, Turicibacter, Veillonella, Vibrio, and Yersinia.

[0021] In some embodiments of any of the methods described herein, the microorganism may be a bacterium of a species selected from the group consisting of Bacteroides fragilis, Bacteroides distasonis, Bacteroides melanogenicus, Bacteroides ovatus, Bacteroides thetaiotamicron, Bacteroides uniformis, Bacteroides urolyticus, Bacteroides vulgatus, Citrobacter diversus, Citrobacter freundii, Citrobacter koseri, Escherichia coli, Enterobacter aerogenes, Klebsiella pneumoniae, Staphylococcus aureus, Shigella dysenteriae, Shigella flexneri, Shigella boydii, Shigella sonnei, Salmonella enterica, Salmonella bongori, Vibrio cholerae, Vibrio vulnificus, Vibrio parahemolyticus, Aeromonas hydrophila, Plesiomonas shigelloides, Prevotella bivia, Prevotella intermedia, Prevotella melanogenica, Proteus mirabilis, Pseudomonas aeruginosa, Haemophilus influenzae, Haemophilus parainfluenzae, Streptococcus agalactiae, Streptococcus mutans, Streptococcus pneumoniae, Streptococcus pyogenes, Enterococcus faecalis, Campylobacter jejuni, Clostridium sporogenes, Helicobacter pylori, Bacillus cereus, Yersinia enterocolitica, and Yersinia pseudotuberculosis.

[0022] In some embodiments of any of the methods described herein, the microorganism may be an archeon of a species selected from the group consisting of Methanobrevibacter smithii, Methanosphaera stadtmanae, and Methanobacterium ruminatum.

[0023] In some embodiments of any of the methods described herein, the methods includes inoculating a culture media with a portion of the sample.

[0024] In some embodiments of any of the methods described herein, the methods include separating (e.g., isolating individual strains) of the microorganisms in the sample.

[0025] In some embodiments of any of the methods described herein, the plurality of microorganisms derived from the microorganism are contacted with the antimicrobial agent in a liquid culture media.

[0026] In some embodiments of any of the methods described herein, the plurality of microorganisms derived from the microorganism are contacted with the antimicrobial agent in a solid culture media.

[0027] In some embodiments of any of the methods described herein, the antimicrobial agent is impregnated on a device having a concentration gradient of the antimicrobial agent.

[0028] In some embodiments of any of the methods described herein, the antimicrobial agent is impregnated on a device having a fixed concentration of the antimicrobial agent.

[0029] Also described herein are antimicrobial agents from the group consisting of a betalactam antibiotic, an aminoglycoside, an ansa-type antibiotic, an anthraquinone, an antibiotic azole, an antibiotic glycopeptide, a macrolide, an antibiotic nucleoside, an antibiotic peptide, an antibiotic polyene, an antibiotic polyether, a quinolone, an antibiotic steroid, a sulfonamide, a carbapenem, tetracycline, a dicarboxylic acid, an antibiotic metal, an oxidizing agent, a substance that releases free radicals, a substance that releases active oxygen, a cationic antimicrobial agent, a quaternary ammonium compound, a biguanide, a triguanide, a bisbiguanide, a naturally-occurring antibiotic compound, an analog thereof, a polymer thereof, or a combination thereof. In some embodiments of any of the methods described herein, the methods include administering the ingestible device to a subject.

[0030] In some embodiments of any of the methods described herein, the methods include collecting the ingestible device from the subject.

[0031] In some embodiments of any of the methods described herein, the methods include removing the sample from the ingestible device.

[0032] In some embodiments of any of the methods described herein, the methods include identifying the microorganism. The microorganism may be identified using dark-field microscopy, electron microscopy, microcolony detection by autofluorescence, fluorescence in situ hybridization (FISH), flow cytometry, a differential system reactivity assays, 16S ribosomal RNA sequencing, 23S ribosomal RNA sequencing, 18S ribosomal RNA sequencing, whole genome sequencing, rpoB gene sequencing, serological testing, PCR, real time PCR, matrix assisted laser desorption ionization time-of-flight (MALDI-TOF), polymerase chain reaction / electrospray ionization mass spectrometry (PCR / ESI-MS), or a combination thereof.

[0033] In some embodiments of any of the methods described herein, the methods include quantifying the amount of the microorganism (e.g., dead and / or live cells) present in the sample.

[0034] In some embodiments of any of the methods described herein, the methods include determining the viability of the microorganism present in the sample.

[0035] In another aspect, the disclosure provides a pharmaceutical formulation for use in a method of preventing regrowth of a bacterium implicated in the pathogenesis of SIBO in a subject in need thereof, the method comprising: orally administering an effective amount of the pharmaceutical formulation, which comprises an antimicrobial agent, to the subject, wherein the antimicrobial agent exhibits antimicrobial activity against a bacterium implicated in the pathogenesis of SIBO; and decreasing the amount of bacterium by at least a 3-log reduction in CFU / mL, as compared to the amount of bacterium at the time of beginning administration of the formulation, wherein exposure of the bacterium to the antimicrobial agent prevents regrowth of the bacterium, wherein the antimicrobial agent is selected from meropenem and ceftriaxone and wherein the pharmaceutical formulation is either: formulated for oral administration as a solid dosage form with an enteric coating; or is administered in an ingestible device and released into the small intestine.

[0036] In some embodiments, the method includes identifying an antimicrobial agent that inhibits the growth of the microorganism, wherein the microorganism has been obtained from a sample having been removed from a ingestible device that retrieved the sample from the GI tract of the subject; and administering an effective amount of a pharmaceutical formulation that includes the identified antimicrobial agent to the subject, thereby treating the infection in the subject.

[0037] In some embodiments, the bacterium is selected from the group consisting of E. coli, Streptococcus spp., Bacteroides spp, or any combination thereof.

[0038] In some embodiments of any of the methods described herein, the microorganism may be a pathogenic microorganism.

[0039] In some embodiments of any of the methods described herein, the microorganism is a protozoan, a bacterium, a parasite, an archeon, or a fungus. In some embodiments, the microorganism is a bacterium of a species selected from the group consisting of Staphylococcus aureus, Shigella dysenteriae, Shigella flexneri, Shigella boydii, Shigella sonnei, Salmonella enterica, Salmonella bongori, Escherichia coli, Vibrio cholerae, Vibrio vulnificus, Vibrio parahemolyticus, Aeromonas hydrophila, Plesiomonas shigelloides, Campylobacter jejuni, Helicobacter pylori, Bacillus cereus, Yersinia enterocolitica, and Yersinia pseudotuberculosis.

[0040] In some embodiments of any of the methods described herein, the ingestible device retrieved the sample from the mouth, the throat, the esophagus, the stomach, the rectum, the anus, the sphincter, the duodenum, the jejunum, the ileum, the ascending colon, the transverse colon, or the descending colon of the subject.

[0041] In some embodiments of any of the methods described herein, the ingestible device retrieved the sample from the jejunum of the subject.

[0042] In some embodiments of any of the methods described herein, the microorganism may be a bacterium from a genus selected from the group consisting of Acetanaerobacterium, Acetivibrio, Aeromonas, Alicyclobacillus, Alkaliphilus, Anaerofustis, Anaerosporobacter, Anaerostipes, Anaerotruncus, Anoxybacillus, Bacillus, Bacteroides, Blautia, Brachyspira, Brevibacillus, Bryantella, Bulleidia, Butyricicoccus, Butyrivibrio, Campylobacter, Catenibacterium, Chlamydiales, Citrobacter, Clostridiales, Clostridium, Collinsella, Coprobacillus, Coprococcus, Coxiella, Deferribacteres, Desulfitobacterium, Desulfotomaculum, Dorea, Eggerthella, Enterobacter, Enterococcus, Escherichia, Erysipelothrix, Erysipelotrichaceae, Ethanoligenens, Eubacterium, Faecalibacterium, Filifactor, Flavonifractor, Flexistipes, Fulvimonas, Fusobacterium, Gemmiger, Geobacillus, Gloeobacter, Haemophilus, Helicobacter, Holdemania, Hydrogenoanaerobacterium, Klebsiella, Kocuria, Lachnobacterium, Lachnospira, Lactobacillus, Lactonifactor, Leptospira, Lutispora, Lysinibacillus, Mollicutes, Moorella, Nocardia, Oscillibacter, Oscillospira, Paenibacillus, Papillibacter, Plesiomonas, Pseudoflavonifractor, Proteus, Pseudomonas, Robinsoniella, Roseburia, Ruminococcaceae, Ruminococcus, Saccharomonospora, Sarcina, Salmonella, Solobacterium, Shigella, Sporobacter, Sporolactobacillus, Streptomyces, Subdoligranulum, Sutterella, Staphylococcus, Streptococcus, Syntrophococcus, Thermoanaerobacter, Thermobifida, Turicibacter, Veillonella, Vibrio, and Yersinia.

[0043] In some embodiments of any of the methods described herein, the microorganism may be a bacterium from a species selected from the group consisting of Bacteroides fragilis, Bacteroides distasonis, Bacteroides melanogenicus, Bacteroides ovatus, Bacteroides thetaiotamicron, Bacteroides uniformis, Bacteroides urolyticus, Bacteroides vulgatus, Citrobacter diversus, Citrobacter freundii, Citrobacter koseri, Escherichia coli, Enterobacter aerogenes, Klebsiella pneumoniae, Staphylococcus aureus, Prevotella bivia, Prevotella intermedia, Prevotella melanogenica, Proteus mirabilis, Pseudomonas aeruginosa, Haemophilus influenzae, Haemophilus parainfluenzae, Streptococcus agalactiae, Streptococcus mutans, Streptococcus pneumoniae, Streptococcus pyogenes, Enterococcus faecalis, and Clostridium sporogenes.

[0044] In some embodiments of any of the methods described herein, the microorganism may be an archeon (e.g., a methanogenic archeon) from a species selected from the group consisting of Methanobrevibacter smithii, Methanosphaera stadtmanae, and Methanobacterium ruminatum.

[0045] In some embodiments of any of the methods described herein, the ingestible device includes a sampling chamber configured to collect the sample from the GI tract of the subject. In some embodiments of any of the methods described herein, the sampling chamber includes the antimicrobial agent.

[0046] In some embodiments of any of the methods described herein, identifying an antimicrobial agent that inhibits the growth of the microorganism includes quantitating and determining the viability of the microorganism obtained from the sample chamber, wherein reduced viability indicates that the microorganism is susceptible to the antimicrobial agent.

[0047] In some embodiments of any of the methods described herein, identifying an antimicrobial agent that inhibits the growth of the microorganism includes contacting a plurality of microorganisms derived from the microorganism with the antimicrobial agent for a predetermined period of time; and detecting growth of the plurality of microorganisms, wherein reduced growth in the presence of the microbial agent relative to a reference indicates that the microorganism is susceptible to the antimicrobial agent, and wherein non-reduced growth in the presence of the microbial agent relative to the reference indicates that the microorganism is resistant to the antimicrobial agent. In some embodiments, the reference includes a plurality of microorganisms derived from the microorganism incubated in the absence of the antimicrobial agent for the predetermined period of time.

[0048] In some embodiments of any of the methods described herein, the ingestible device includes a microprocessor.

[0049] In some embodiments of any of the methods described herein, the ingestible device includes a housing, and the sample chamber is configured within the housing such that, when the device is in the GI tract of the subject, the sample chamber is in selective fluid communication with the GI tract. In some embodiments of any of the methods described herein, the housing is not biodegradable in the GI tract.

[0050] In some embodiments of any of the methods described herein, the sampling chamber of the ingestible device includes an absorptive material.

[0051] In some embodiments of any of the methods described herein, the subject is a human subject.

[0052] In some embodiments of any of the methods described herein, the methods include inoculating a culture media with a portion of the sample.

[0053] In some embodiments of any of the methods described herein, the methods include separating the microorganisms in the sample.

[0054] In some embodiments of any of the methods described herein, the plurality of microorganisms derived from the microorganism are contacted with the antimicrobial agent in a solid culture media (e.g., an agar plate). In some embodiments of any of the methods described herein, the plurality of microorganisms derived from the microorganism are contacted with the antimicrobial agent in a liquid culture media (e.g., a liquid culture broth).

[0055] In some embodiments of any of the methods described herein, the antimicrobial agent is impregnated on a device having a concentration gradient of the antimicrobial agent.

[0056] In some embodiments of any of the methods described herein, the antimicrobial agent is impregnated on a device having a fixed concentration of the antimicrobial agent.

[0057] Also described herein are antimicrobial agents from the group consisting of a betalactam antibiotic, an aminoglycoside, an ansa-type antibiotic, an anthraquinone, an antibiotic azole, an antibiotic glycopeptide, a macrolide, an antibiotic nucleoside, an antibiotic peptide, an antibiotic polyene, an antibiotic polyether, a quinolone, an antibiotic steroid, a sulfonamide, a carbapenem, tetracycline, a dicarboxylic acid, an antibiotic metal, an oxidizing agent, a substance that releases free radicals, a substance that releases active oxygen, a cationic antimicrobial agent, a quaternary ammonium compound, a biguanide, a triguanide, a bisbiguanide, a naturally-occurring antibiotic compound, an analog thereof, a polymer thereof, and a combination thereof.

[0058] Also described herein are antimicrobial agents from the group consisting of a cephalosporin, a quinolone, tetracycline, ampicillin, erythromycin, rifaximin, metronidazole, erythromycin, amoxicillin-clavulanic acid, cefoxitin, ciprofloxacin, norfloxacin, neomycin, doxycycline, lincomycin, chloramphenicol, ertapenem, meropenem, ceftriaxone, piperacillin, and tazobactam.

[0059] The antimicrobial agent of the present invention is selected from the group consisting of meropenem or ceftriaxone. Also described herein are antimicrobial agents such as ertapenem, and piperacillin-tazobactam.

[0060] In some embodiments of any of the methods described herein, the methods include administering the ingestible device to the subject.

[0061] In some embodiments of any of the methods described herein, the methods include collecting the ingestible device from the subject.

[0062] In some embodiments of any of the methods described herein, the methods include removing the sample from the ingestible device.

[0063] In some embodiments of any of the methods described herein, the methods include identifying the microorganism. The microorganism may be identified using dark-field microscopy, electron microscopy, microcolony detection by autofluorescence, fluorescence in situ hybridization (FISH), flow cytometry, a differential system reactivity assays, 16S ribosomal RNA sequencing, 23S ribosomal RNA sequencing, 18S ribosomal RNA sequencing, whole genome sequencing, rpoB gene sequencing, serological testing, PCR, real time PCR, matrix assisted laser desorption ionization time-of-flight (MALDI-TOF), polymerase chain reaction / electrospray ionization mass spectrometry (PCR / ESI-MS), or a combination thereof.

[0064] In some embodiments of any of the methods described herein, the methods include quantifying the amount of the microorganism present in the sample.

[0065] In some embodiments of any of the methods described herein, the methods include determining the viability of the microorganism present in the sample.

[0066] Also described herein are pharmaceutical composition that can be administered to the subject orally, rectally, or intravenously. Also described herein are pharmaceutical composition that can be administered to the subject parenterally. In some embodiments of any of the methods described herein, the pharmaceutical formulation may be in a solid dosage form or a liquid dosage form.

[0067] The pharmaceutical formulation may be administered in an ingestible device described herein.

[0068] The pharmaceutical formulation is released from an ingestible device described herein. In some disclosures, the pharmaceutical formulation is released at the mouth, the throat, the esophagus, the stomach, the rectum, the anus, the sphincter, the duodenum, the jejunum, the ileum, the ascending colon, the transverse colon, or the descending colon of the subject. disclosures, the pharmaceutical formulation is released at a location in the gastrointestinal tract of the subject that is proximate to one or more sites of disease (e.g., the small intestine (e.g., jejunum) of the subject).

[0069] In some embodiments of any of the methods described herein, the ingestible device includes a housing, a reservoir containing the pharmaceutical formulation, and a release mechanism for releasing the pharmaceutical formulation from the second ingestible device. In some embodiments, the ingestible device may include a microprocessor. In some embodiments, the housing that is not biodegradable in the GI tract.

[0070] The disclosure also provides methods for identifying a microorganism present in the gastrointestinal (GI) tract of a subject, the methods include performing a test to identify the microorganism, wherein the microorganism has been obtained from a sample having been removed from a ingestible device that retrieved the sample from the GI tract of the subject.

[0071] In some embodiments of any of the methods described herein, the ingestible device includes a sampling chamber configured to collect the sample from the GI tract of the subject. In some embodiments of any of the methods described herein, the sampling chamber includes an absorptive material. In some embodiments of any of the methods described herein, the ingestible device includes a microprocessor.

[0072] In some embodiments of any of the methods described herein, the test to identify the microorganism may be dark-field microscopy, electron microscopy, microcolony detection by autofluorescence, fluorescence in situ hybridization (FISH), flow cytometry, a differential system reactivity assays, 16S ribosomal RNA sequencing, 23S ribosomal RNA sequencing, 18S ribosomal RNA sequencing, whole genome sequencing, rpoB gene sequencing, serological testing, PCR, real time PCR, matrix assisted laser desorption ionization time-of-flight (MALDI-TOF), polymerase chain reaction / electrospray ionization mass spectrometry (PCR / ESI-MS), or a combination thereof.

[0073] In some embodiments of any of the methods described herein, the ingestible device includes a housing, and the sample chamber is configured within the housing such that, when the device is in the GI tract of the subject, the sample chamber is in selective fluid communication with the GI tract. In some embodiments, the housing is not biodegradable in the GI tract.

[0074] In some embodiments of any of the methods described herein, the ingestible device retrieved the sample from the mouth, the throat, the esophagus, the stomach, the rectum, the anus, the sphincter, the duodenum, the jejunum, the ileum, the ascending colon, the transverse colon, or the descending colon of the subject.

[0075] In some embodiments of any of the methods described herein, the subject is a human subject. In some embodiments, the human subject has symptomology of a gastrointestinal disorder. In some embodiments, the human subject has been diagnosed with a gastrointestinal disorder.

[0076] In some embodiments of any of the methods described herein, the microorganism may be a commensal microorganism or a pathogenic microorganism. In some embodiments, the microorganism may be a bacterium, an archaeon, a protozoan, a parasite, or a fungus.

[0077] In some embodiments of any of the methods described herein, the methods include inoculating a culture media with a portion of the sample.

[0078] In some embodiments of any of the methods described herein, the methods include separating the microorganisms in the sample.

[0079] In some embodiments of any of the methods described herein, the methods include administering the ingestible device to a subject.

[0080] In some embodiments of any of the methods described herein, the methods include collecting the ingestible device from the subject.

[0081] In some embodiments of any of the methods described herein, the methods include removing the sample from the ingestible device.

[0082] In some embodiments of any of the methods described herein, the methods include quantifying the amount of the microorganism (e.g., live and / or dead cells) present in the sample. In some embodiments of any of the methods described herein, the methods include determining the viability of the microorganism present in the sample.

[0083] In yet another aspect, the disclosure provides a pharmaceutical formulation for use in a method of preventing the development of resistance to treatment by an antimicrobial agent of a bacterium implicated in the pathogenesis of SIBO in a subject in need thereof, the method comprising: orally administering an effective amount of a pharmaceutical formulation, which comprises the antimicrobial agent, to the subject, wherein the antimicrobial agent is meropenem or ceftriaxone and wherein the pharmaceutical formulation is either: formulated for oral administration as a solid dosage form with an enteric coating; or is administered in an ingestible device and released into the small intestine, and wherein the bacterium has a spontaneous mutation frequency of less than 7.45×10 -9< , 5.75×10 -9< , 5.15×10 -9< , 9.55×10 -10< , 1.85×10 -10< , 1.75×10 -10< , 1.50×10 -10< , or 1.05×10 -10< .BRIEF DESCRIPTION OF THE DRAWINGS

[0084] Exemplary embodiments of the disclosure are provided below with reference to the drawings. FIG. 1 shows an ingestible device. FIG. 2 shows an ingestible device. FIG. 3 shows a valve. FIGs. 4 and 5 illustrate operation of a valve. FIG. 6 shows an ingestible device. FIG. 7 shows valve designs. FIG. 8 shows a sampling chamber. FIG. 9 shows a pumping mechanism. FIG. 10 shows an ingestible device. FIG. 11 shows an ingestible device. FIG. 12 illustrates a valve system. FIGs. 13A and 13B illustrate a portion of a two-stage valve system in its first and second stages, respectively. FIGs. 14Aand 14B illustrate a portion of a two-stage valve system in its first and second stages, respectively. FIGs. 15A and 15B illustrate a portion of a two-stage valve system in its first and second stages, respectively. FIG. 16 illustrates a more detailed view of an ingestible device. FIGs. 17A-17C illustrate a portion of a three-stage valve system in its first, second and third stages, respectively. FIGs. 18A-18C illustrate a portion of a three-stage valve system in its first, second and third stages, respectively. FIGs. 19A-19C illustrate a portion of a three-stage valve system in its first, second and third stages, respectively. FIG. 20 illustrates a three-stage valve system in its first stage. FIG. 21A illustrates a portion of an ingestible device. FIG. 21B illustrates a portion of an ingestible device. FIG. 22 illustrates an ingestible device. FIG. 23 illustrates an ingestible device. FIG. 24 illustrates an ingestible device. FIG. 25 illustrates an ingestible device. FIG. 26 is an exploded view of an ingestible device. FIG. 27 illustrates a portion of an ingestible device. FIG. 28 illustrates a portion of an ingestible device. FIG. 29 illustrates a member forming part of a set of five incubation chambers suitable for an ingestible device. FIG. 30 illustrates a partial cross-sectional view of optics in an ingestible device. FIG. 31 illustrates components of the optics and flow chamber systems in an ingestible device. FIG. 32 shows a partial view of an ingestible device FIGs. 33A, 33B and 33C illustrate operation of ingestible device. FIG. 34 illustrates an exploded view of the components of ingestible device. FIG. 35 illustrates an ingestible device. FIG. 36 illustrates aspects of a mechanism for an ingestible device. FIG. 37 illustrates an ingestible device. FIG. 38 illustrates an ingestible device. FIG. 39 illustrates an ingestible device. FIGs. 40, 41 and 42 illustrate exemplary anchoring mechanisms of an ingestible device. FIG. 43 illustrates an ingestible device. FIG. 44A illustrates a portion of an ingestible device. FIG. 44B illustrates a partial sectional view of a burst disc holder. FIG. 45 illustrates an ingestible device. FIG. 46 illustrates an ingestible device. FIG. 47 illustrates an ingestible device. FIG. 48 illustrates an ingestible device. FIG. 49 illustrates an ingestible device. FIG. 50 illustrates an ingestible device. FIG. 51 illustrates an ingestible device. FIG. 52 illustrates an ingestible device. FIG. 53 illustrates an ingestible device. FIG. 54 illustrates an ingestible device. FIG. 55 illustrates an ingestible device. FIG. 56 is a view of an ingestible device. FIG. 57 is an exploded view of an ingestible device. FIG. 58 is a diagram of an ingestible device during an example transit through a GI tract. FIG. 59 is a diagram of an ingestible device during an example transit through a jejunum. FIG. 60 is a flowchart of illustrative steps for determining a location of an ingestible device as it transits through a GI tract. FIG. 61 is a flowchart of illustrative steps for detecting transitions from a stomach to a duodenum and from a duodenum back to a stomach. FIG. 62 is a plot illustrating data collected during an example operation of an ingestible device. FIG. 63 is another plot illustrating data collected during an example operation of an ingestible device. FIG. 64 is a flowchart of illustrative steps for detecting a transition from a duodenum to a jejunum. FIG. 65 is a plot illustrating data collected during an example operation of an ingestible device. FIG. 66 is a plot illustrating muscle contractions detected by an ingestible device over time. FIG. 67 is a flowchart of illustrative steps for detecting a transition from a jejunum to an ileum. FIG. 68 is a flowchart of illustrative steps for detecting a transition from a jejunum to an ileum. FIG. 69 is a flowchart of illustrative steps for detecting a transition from an ileum to a cecum. FIG. 70 is a flowchart of illustrative steps for detecting a transition from a cecum to a colon. FIG. 71 shows an embodiment of an exemplary ingestible device including a spectrometer and a separate base station. FIG. 72 illustrates an exemplary system for collecting, communicating and / or analyzing data about a subject. FIG. 73 shows an illustrative embodiment of a method for extracting a sample from an ingestible device. FIG. 74 shows an illustrative embodiment of a method for creating an opening in an ingestible device using a heated lancet, which may be used in conjunction with the method illustrated by FIG. 73. FIG. 75 shows an illustrative embodiment of a lancing device, which may be used to create an opening in an ingestible device, and may be used in conjunction with the method illustrated by FIG. 73. FIG. 76 shows an illustrative embodiment of a grating device, which may be used to create an opening in an ingestible device, and may be used in conjunction with the method illustrated by FIG. 73. FIG. 77 shows an illustrative embodiment of a sleeve device, which may connect the ingestible device to a tube, and may be used in conjunction with the method illustrated by FIG. 73. FIG. 78 shows an illustrative embodiment of a centrifuge mechanism, which may allow the sleeve device and the ingestible device to be inserted into a centrifuge, and may be used in conjunction with the method illustrated by FIG. 73. FIG. 79 shows another illustrative embodiment of a centrifuge mechanism, which may allow the sleeve device and the ingestible device to be inserted into a centrifuge, and may be used in conjunction with the method illustrated by FIG. 73. FIG. 80 shows an illustrative embodiment of a method for separating the ingestible device into multiple portions, and extracting a sample from a portion of the ingestible device. FIG. 81 shows an illustrative embodiment of an adapter device, which may connect a portion of an ingestible device to a tube, and may be used in conjunction with the method illustrated by FIG. 80. FIG. 82 illustrates a system for extracting a sample from an ingestible device. FIG. 83 is a partial exploded view of the system illustrated in FIG. 82. FIGs. 84A and 84B illustrate views of an ingestible device with holes for allowing sample to exit samples chambers in the device. FIG. 85 illustrates a cross-sectional view of an ingestible device with holes for allowing sample to exit samples chambers in the device. FIG. 86 illustrates an exemplary pathway for the diagnosis and treatment of gastrointestinal disorder symptomology. FIG. 87 illustrates an exemplary pathway for the diagnosis and treatment of SIBO. FIG. 88 illustrates an exemplary pathway for the diagnosis and treatment of IBS. FIG. 89 illustrates an exemplary pathway for the diagnosis and treatment of a subject having IBS symptomology. FIG. 90 illustrates an exemplary pathway for the diagnosis and treatment of a patient having abdominal pain or discomfort. FIG. 91 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 50 Enterobacter aerogenes clinical isolates (µg / mL). FIG. 92 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 50 Escherichia coli clinical isolates (µg / mL). FIG. 93 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 50 Klebsiella spp. clinical isolates (µg / mL). FIG. 94 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 50 Proteus mirabilis clinical isolates (µg / mL). FIG. 95 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 50 Pseudomonas aeruginosa clinical isolates (µg / mL). FIG. 96 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 50 Staphylococcus aureus clinical isolates (µg / mL). FIG. 97 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 50 Enterococcus faecalis clinical isolates (µg / mL). FIG. 98 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 54 Streptococcus spp. (n = 19 S. pyogenes, n = 20 S. agalactiae and n = 20 Viridans group Streptococcus) clinical isolates (µg / mL). FIG. 99 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 19 Streptococcus pyogenes clinical isolates (µg / mL). FIG. 100 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 20 Streptococcus agalactiae clinical isolates (µg / mL). FIG. 101 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 15 Viridans group Streptococci clinical isolates (µg / mL). FIG. 102 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 10 Clostridium spp. (n = 4 C. sporogenes, n = 2 C. ramosum and n = 4 C. innocuum) clinical isolates (µg / mL). FIG. 103 Meropen shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 30 Prevotella spp. (n = 5 P. melaninogenica, n = 7 P. bivia, n = 11 P. buccae, and n = 1 each P. intermedia, P. nanceiensis, P. denticola, P. nigrescens, P. corporis, P. bergensis, and P. disiens) clinical isolates (µg / mL). FIG. 104 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 30 Veillonella spp. (n = 19 V. parvula, n = 9 Veillonella spp., n = 1 Veillonella dispr., n = 1 V. atypica) clinical isolates (µg / mL). FIG. 105 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 30 Bacteroides fragilis clinical isolates (µg / mL). FIG. 106 shows meropenem (MEM), ceftriaxone (CTR), and rifaximin (RFX) MIC distribution against 29 Bacteroides non-fragilis (n = 3 B. caccae, n = 7 B. thetaiotaomicron, n = 4 B. ovatus, n = 5 B. vulgatus, n = 2 B. uniformis, n = 2 B. stercoris, n = 1 B. salversiae, n = 1 B. intestinalis, n = 3 B. xylanisolveris, and n = 1 B. faecis) clinical isolates (µg / mL). FIGs. 107A-107C show the time-kill kinetics of meropenem (MEM; FIG. 107A), ceftriaxone (CRO; FIG. 107B) and rifaximin (RFX; FIG. 107C) against E. coli ATCC 25922. FIGs. 108A-108C show the time-kill kinetics of meropenem (MEM; FIG. 108A), ceftriaxone (CRO; FIG. 108B) and rifaximin (RFX; FIG. 108C) against E. coli ATCC 35218. FIGs. 109A-109C show the time-kill kinetics of meropenem (MEM; FIG. 109A), ceftriaxone (CRO; FIG. 109B) and rifaximin (RFX; FIG. 109C) against E. coli MMX 1312. FIGs. 110A-110C show the time-kill kinetics of meropenem (MEM; FIG. 110A), ceftriaxone (CRO; FIG. 110B) and rifaximin (RFX; FIG. 110C) against S. pneumoniae ATCC 49619. FIGs. 111A-111C show the time-kill kinetics of meropenem (MEM; FIG. 111A), ceftriaxone (CRO; FIG. 111B) and rifaximin (RFX; FIG. 111C) against S. pyogenes ATCC 49399. FIGs. 112A-112C show the time-kill kinetics of meropenem (MEM; FIG. 112A), ceftriaxone (CRO; FIG. 112B) and rifaximin (RFX; FIG. 112C) against S. agalactiae ATCC 13813. FIGs. 113A-113B show the time-kill kinetics of meropenem (MEM; FIG. 113A) and rifaximin (RFX; FIG. 113B) against B. fragilis ATCC 25285. FIGs. 114A-114C show the time-kill kinetics of meropenem (MEM; FIG. 114A), ceftriaxone (CRO; FIG. 114B) and rifaximin (RFX; FIG. 114C) against B. vulgatus ATCC 8482. FIGs. 115A-115B show the time-kill kinetics of meropenem (MEM; FIG. 115A) and rifaximin (RFX; FIG. 115B) against B. ovatus MMX 3503. DETAILED DESCRIPTION

[0085] Various apparatuses, systems, devices, components and / or processes will be described below to provide illustrative and non-limiting examples. No embodiment described below limits the subject matter covered by any claim, and any claim may cover processes or apparatuses that differ from those described below. As an example, the subject matter covered by the claims is not limited to apparatuses, systems, devices, components and / or processes having all of the features of any one apparatus, system, device, component and / or process described below or to features common to multiple or all of the apparatuses or processes described below. It is possible that a given apparatus, system, device, component and / or or process described below is not covered by a given claim. Any embodiment disclosed herein that is not covered by one or more claims in this document may be covered by one or more claims in one or more other protective instruments, such as, for example, one or more continuing patent applications and / or one or more divisional patent applications. The Applicants, inventors and / or owners do not necessarily intend to abandon, disclaim or dedicate to the public any subject matter disclosed herein but not covered by a claim herein.

[0086] Furthermore, it will be appreciated that for simplicity and clarity of illustration, where considered appropriate, reference numerals may be repeated among the figures to indicate corresponding or analogous elements. In addition, numerous specific details are set forth in order to provide a thorough understanding of the embodiments described herein. However, it is to be understood that the embodiments described herein may be practiced without these specific details. In other instances, well-known methods, procedures and components may have not been described in detail so as not to obscure the embodiments described herein. Also, the description is not to be considered as limiting the scope of the embodiments described herein.Definitions

[0087] Unless otherwise defined herein, scientific and technical terms used in this disclosure shall have the meanings that are commonly understood by those of ordinary skill in the art. Generally, nomenclature used in connection with, and techniques of, chemistry, cell and tissue culture, molecular biology, cell and cancer biology, neurobiology, neurochemistry, virology, immunology, microbiology, pharmacology, genetics and protein and nucleic acid chemistry, described herein, are those well-known and commonly used in the art.

[0088] The methods and techniques of the present disclosure are generally performed, unless otherwise indicated, according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout this specification.

[0089] Chemistry terms used herein are used according to conventional usage in the art, as exemplified by "The McGraw-Hill Dictionary of Chemical Terms," Parker S., Ed., McGraw-Hill, San Francisco, C.A. (1985).

[0090] In case of conflict between the disclosures of the publications, patents and published patents referred to herein, the present specification, including its specific definitions, will control.

[0091] A "patient," "subject," or "individual" are used interchangeably and refer to either a human or a non-human animal. These terms include mammals, such as humans, primates, livestock animals (including bovine, porcine, etc.), companion animals (e.g., canine, feline, etc.) and rodents (e.g., mice and rats). The term "animal" refers to humans (male or female), companion animals (e.g., dogs, cats and horses), food-source animals, zoo animals, marine animals, birds and other similar animal species. "Edible animals" refers to food-source animals such as cows, pigs, sheep and poultry.

[0092] The terms "treating," "treat," or "treatment" embrace both preventative, i.e., prophylactic, and palliative treatment. For example, treating can refer to inhibiting the disease; e.g., inhibiting a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomology of the disease, condition or disorder (i.e., arresting further development of the pathology and / or symptomology). Treating can also refer to ameliorating the disease; e.g., ameliorating a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomology of the disease, condition or disorder (i.e., reversing the pathology and / or symptomology) such as decreasing the severity of disease. Treating can also include preventing or reducing the risk of developing the disease; e.g., preventing or reducing the risk of developing a disease, condition or disorder in an individual who may be predisposed to the disease, condition or disorder but does not yet experience or display the pathology or symptomology of the disease.

[0093] The methods described herein include the use of an ingestible device for detecting markers (e.g., bacteria) associated with symptomology of a functional bowel disorder in a subject who has or is at risk of developing a functional bowel disorder. In some disclosures, the subject has been previously identified as having a functional bowel disorder. In some disclosures, the subject has one or more symptoms of a functional bowel disorder. Some disclosures of any of the methods provided herein further include, prior to the providing an ingestible device step, determining that the subject has a functional bowl disorder. Some disclosures of any of the methods can further include identifying or diagnosing a subject as having a functional bowel disorder.

[0094] "Eukaryotic" as recited herein relates to any type of eukaryotic organism excluding fungi, such as animals, in particular animals containing blood, and includes invertebrate animals such as crustaceans and vertebrates. Vertebrates include both cold-blooded (fish, reptiles, amphibians) and warm blooded animal (birds and mammals). Mammals include in particular primates and more particularly humans.

[0095] "Microbiota" or "microbiome" as used herein refers to the community of microorganisms present in and on a human subject, including single cell and multicellular eukaryotes such as protozoan, helminthic and fungal eukaryotes, archaea, bacteria, and viruses (including bacterial viruses, i.e., phage).

[0096] "Selective lysis" as used in the present disclosure is obtained in a sample when a certain type of cell (e.g., a bacterial and / or archaeal cell (e.g., a Gram-positive or a Gram-negative bacterial cell) or a eukaryotic cell) is preferentially lysed over a different type of cell in the sample (e.g., eukaryotic cell or a bacterial cell). In some disclosures, cells of a particular genera, species or strain are preferentially lysed over cells of a different genera, species or strain. In some disclosures, the percentage of cells of a first genera, species, or strain in the sample that remain intact is significantly higher (e.g., 2, 5, 10, 20, 50, 100, 250, 500, or 1,000 times more) than the percentage of cells of a second genera, species, or strain in the sample that remain intact, upon treatment of or contact with a composition or device as described herein. In some disclosures, the percentage of the bacterial and / or archaeal cells in the sample is significantly lower (e.g., 2, 5, 10, 20, 50, 100, 250, 500, or 1,000 times less) than the percentage of the eukaryotic cells in the sample that remain intact, upon treatment of or contact with a composition or device described herein. In some disclosures, the percentage of bacterial and / or archaeal cells in the sample that remain intact is significantly higher (e.g., 2, 5, 10, 20, 50, 100, 250, 500, or 1,000 times more) than the percentage of the eukaryotic cells in the sample that remain intact, upon treatment of or contact with a composition or device as described herein. In some disclosures, the percentage of Gram-positive bacterial cell in the sample that remain intact is significantly higher (e.g., 2, 5, 10, 20, 50, 100, 250, 500, or 1,000 times more) than the percentage of the Gram-negative bacterial cells in the sample that remain intact, upon treatment of or contact with a composition or device as described herein. In some disclosures, the percentage of Gram-negative bacterial cell in the sample that remain intact is significantly higher (e.g., 2, 5, 10, 20, 50, 100, 250, 500, or 1,000 times more) than the percentage of the Gram-positive bacterial cells in the sample that remain intact, upon treatment of or contact with a composition or device as described herein.

[0097] A "sample" as used in the present disclosure may be a biological sample or an environmental sample. Such samples may be obtained from any organism or environmental site desired. For example, the compositions, methods and devices of this disclosure may be used for detecting and quantifying bacterial and / or archaeal cells in a sample obtained from, without limitation, soil, rock, plants, animals, cell or tissue culture, biofilms, organic debris, or water. In some disclosures, samples are obtained from mammals such as humans. In some embodiments, samples are obtained from a human's GI tract. In some disclosures, samples are body fluid samples including, but not limited to urine, blood, plasma, serum, saliva, semen, stool, sputum, cerebral spinal fluid, tears, mucus, and the like. In some disclosures, a single device collects multiple samples, for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 100 or more samples. In some disclosures, the sample is between 1-2000 µL (e.g., 1-1500 µL, 1-1900 µL, 1-1000 µL, 1-500 µL, 1-250 µL, 1-100 µL, 1-50 µL, 1-10 µL, and 1-5 µL). In some disclosures, samples are tissue samples, for example, from the gastrointestinal tract collected during endoscopy using punch biopsy forceps.

[0098] A "colony-forming unit" or "CFU" refers to a unit used to estimate the number of viable bacterial, archaeal and / or fungal cells in a sample. Viable is defined by the cell's ability to divide and form a population (or colony).

[0099] As used herein, the term "coupled" indicates that two elements can be directly coupled to one another or coupled to one another through one or more intermediate elements.

[0100] The term "saturate" means to permeate or be permeated with a liquid. In some disclosures, an absorptive sponge of the present disclosure may be fully saturated with an amount of a liquid such that no more liquid can be held. In some disclosures, an absorptive sponge of the present disclosure may be partially saturated with a liquid at an amount that is less than the maximum amount of the liquid that can be held by the sponge. For instance, in some disclosures, a sponge is half-saturated with a liquid at half of the maximum amount of the liquid that can be held by the sponge.

[0101] The term "semi-solid" means a material that is neither solid (elastic behavior) nor liquid (viscous behavior) and possesses the characteristics of both viscosity and elasticity. Examples of semi-solid materials include gels, ointments, creams, and highly viscous liquids.

[0102] As used herein "culturing" refers to maintaining cells in an environment that allows a population of one or more cells to increase in number through cell division. For example, in some disclosures "culturing" may include combining the cells with media in a dilution chamber at a temperature that permits cell growth, optionally a temperature found in vivo within the GI tract of a subject. In some disclosures, the cells are cultured at a temperature between about 35 °C and 42 °C. In some disclosures, the cells are cultured at a temperature of about 37 °C.

[0103] As used herein "dilution fluid" refers to a fluid within the device for diluting a fluid sample from the GI tract. In some disclosures, the dilution fluid is an aqueous solution. In some disclosures, the dilution fluid includes one or more agents that promote or inhibit the growth of an organism, such as a fungus or bacteria. In some disclosures, the dilution fluid includes one or more agents that facilitate the detection of an analyte, such as dyes or binding agents for analytes.

[0104] In some disclosures, a dilution fluid is a sterile media. As used herein, "sterile media" refers to media that does not contain any viable bacteria, archaea, or other cells that would grow and increase in number through cell division. Media may be rendered sterile by various techniques known in the art such as, but not limited to, autoclaving and / or preparing the media using aseptic techniques. In some disclosures, the media is a liquid media. Examples of media suitable for culturing bacteria and / or archaea include nutrient broth, Lysogeny Broth (LB) (also known as Luria Broth), Wilkins chalgren, and Tryptic Soy Broth (TSB). Other growth or culture media known in the art may also be used in the methods and devices described herein. In some disclosures, the media has a carbon source, such as glucose or glycerol, a nitrogen source such as ammonium salts or nitrates or amino acids, as well as salts and / or trace elements and vitamins for microbial growth. In some disclosures, the media is suitable for maintaining eukaryotic cells. In some disclosures, the media includes one or more agents that promote or inhibit the growth of bacteria and / or archaea, optionally agents that promote or inhibit the growth of specific types of bacteria and / or archaea.

[0105] In some disclosures, the media is a selective media. As used herein, "selective media" refers to a media that allows certain types of cells to grow and inhibits the growth of other organisms. Accordingly, the growth of cells in a selective media indicates the presence of certain types of cells within the cultured sample. For example, in some disclosures the media is selective for Gram-positive or Gram-negative bacteria. In some disclosures, the media contains crystal violet and bile salts (such as found in MacConkey agar) that inhibit the growth of Gram-positive organisms and allows for the selection and isolation of Gram-negative bacteria. In another disclosures, the media contains a high concentration of salt (e.g., NaCl) (such as found in Mannitol salt agar) and is selective for Gram-positive bacteria. In some disclosures, the media selectively kills eukaryotic cells or only grows prokaryotic cells. In another disclosures, the media selectively kills prokaryotic cells (or alternatively only grows eukaryotic cells), for example, using a media that includes antibiotics.

[0106] In some disclosures, the media is an indicator media. As used herein, "indicator media" refers to a media that contains specific nutrients or indicators (such as, but not limited to neutral red, phenol red, eosin y, or methylene blue) that produce a detectable signal when a certain type of cells are cultured in the indicator media.

[0107] As used herein, "detecting bacteria and / or archaea" refers to determining the presence or absence of bacteria and / or archaea within a sample or estimating the concentration of bacteria and / or archaea within a sample. For example, in some disclosures, bacterial and / or archaeal growth can be determined based on the concentration of bacteria and / or archaea within a sample. In some disclosures, the detection system detects and / or quantitates a particular bacterial and / or archaeal genus, species or strain within a sample. In some disclosures, the detection system detects the products of bacterial and / or archaeal growth within the cultured and / or diluted sample or a change in concentration of certain components within the media due to bacterial and / or archaeal growth. In some disclosures, products of bacterial and / or archaeal growth include analytes produced and / or secreted by the bacteria and / or archaea that are present in the media, including, but not limited to, bacterial toxins, exosomes, secreted proteins, and metabolites.

[0108] A "photosensitizer" as used herein refers to a sensitizer for generation of singlet oxygen usually by excitation with light. Exemplary photosensitizers suitable for use in the present application include those described in U.S. Patent Nos. 6,251,581, 5,516,636, 8,907,081, 6,545,012, 6,331,530, 8,247,180, 5,763,602, 5,705,622, 5,516,636, 7,217,531, and U.S. Patent Publication No. 2007 / 0059316. The photosensitizer can be photoactivatable (e.g., dyes and aromatic compounds) or chemiactivated (e.g., enzymes and metal salts). When excited by light, the photosensitizer is usually a compound included of covalently bonded atoms, usually with multiple conjugated double or triple bonds. The compound should absorb light in the wavelength range of 200-1100 nm, usually 300-1000 nm, e.g., 450-950 nm, with an extinction coefficient at its absorbance maximum greater than 500 M -1< cm -1< , e.g., at least 5000 M -1< cm- 1< , or at least 50,000 M -1< cm -1< at the excitation wavelength. The lifetime of an excited state produced following absorption of light in the absence of oxygen will usually be at least 100 nsec, e.g., at least 1 µsec. In general, the lifetime is desirably sufficiently long to permit energy transfer to oxygen, which will normally be present at concentrations in the range of 10 -5< to 10 -13< M depending on the medium. The sensitizer excited state will usually have a different spin quantum number (s) than its ground state and will usually be a triplet (s=l) when, as is usually the case, the ground state is a singlet (s=0). In some disclosures, the sensitizer will have a high intersystem crossing yield. That is, photoexcitation of a sensitizer will produce the long lived state (usually triplet) with an efficiency of at least 10%, at least 40%, e.g., greater than 80%. The photosensitizer will usually be at most weakly fluorescent under the assay conditions (quantum yield usually less than 0.5, or less than 0.1).

[0109] As used herein, the term "gastrointestinal tract" or "GI tract" refers to all portions of an organ system responsible for consuming and digesting foodstuffs, absorbing nutrients, and expelling waste. This includes orifices and organs such as the mouth, throat, esophagus, stomach, small intestine, large intestine, rectum, anus, and the like, as well as the various passageways and sphincters connecting the aforementioned parts. The device may be used to detect, analyze and / or quantify an analyte, e.g., bacterial cells, in a sample from the GI tract (e.g., in one or more of the mouth, throat, esophagus, stomach, small intestine, large intestine, rectum, anus, sphincter, duodenum, jejunum, ileum, ascending colon, transverse colon, and descending colon, or subsections thereof, for example the proximal jejunum or terminal ileum) of a subject. The device may also be used to detect or quantify bacterial and / or archaeal cells from outside the GI tract. In some disclosures, the samples from the subject are environmental samples that do not contain eukaryotic cells.

[0110] The GI tract is a large organ that extends from the buccal cavity to the anus. The primary function of the GI tract is to digest food, absorb nutrients and eliminated any waste. The GI tract is composed of the esophagus, the stomach, and the intestines. The different segments of the GI tract are generally associated with different characteristics. Chewed food flows through the esophagus, and into the stomach where it is temporarily stored and mixed with gastric acid. Involuntary muscle contractions, termed peristalsis, push the food out of the stomach and into the small intestine. The small intestine can be divided into the duodenum, the jejunum and the ileum. The majority of food digestion and absorption occurs in the ileum. Waste and unwanted products are passed into the colon, or large intestine. Typically, food resides for 10 to 14 seconds in the esophagus, and travels within the small intestine for 2 to 4 hours. Half of the contents of the stomach is emptied within 60 to 90 minutes (Khutoryanskiy (2015) Nature Materials 14:963-964). While food enters the esophagus at approximately pH 7.0, foods are acidified within the stomach (pH 1-5). The pH in the proximal small intestine is between 6.8 and 7.88; between 5.26 and 6.72 in the distal small intestine, between 5.26-6.72 in the ascending colon, and between 5.20 and 7.02 in the descending colon (Khutoryanskiy (2015) Nature Materials 14:963-964).

[0111] Over 1000 different microbial species have been identified that can live in the human GI tract, e.g., Actinobacteria, Bifidobacterium spp., Coriobacteriales, Eggerthella, Slackia spp., Actinomycetales, Bacteroidetes, Firmicutes, Gemella, Clostridia, Lachnospiraceae, Negativicutes, Fusobacteria, and fungi (e.g., Eukarya). See, e.g., Rajilic-Stojanovic and de Vos (2014) FEMS Microbiol. Rev. 38(5):996-1047; and Carroll et al. (2015) Mamm. Genome 20(7):395-403. Whereas the small intestine contains very few bacteria, the colon comprises between 10 13< and 10 14< commensal bacteria (Johansson et al. (2013) Nat. Rev. Gastroenterol. Hepatol. 10(6):352-361).

[0112] The intestinal fluid can contain a variety of digestive enzymes (e.g., pepsin, lipase, amylase, enterokinase, sucrose, maltase, lactase, secretin, motilin). See, e.g., Ulleberg et al. (2011) Food Dig. 2(1-3):52-61.

[0113] As used herein, "minimum inhibitory concentration" or "MIC" refers to the lowest concentration of an antimicrobial agent, for example, an antimicrobial agent as described herein, required to inhibit the growth of an organism. The organism is a bacterium implicated in the pathogenesis of SIBO. "MIC 50 ," as used herein, is the MIC value at which ≥50% of the isolates in a test population are inhibited; it is equivalent to the median MIC value. "MIC 90 " represents the MIC value at which ≥90% of the strains within a test population are inhibited; the 90th percentile.

[0114] "Bactericidal activity," as used herein, refers to a reduction in colony forming units (CFU) per mL after drug (e.g., antimicrobial agent) exposure. In some embodiments, the reduction is a ≥3 log reduction in CFU / mL after about 24 hours of drug (e.g., antimicrobial agent) exposure.

[0115] As used herein, "spontaneous mutation frequency" refers to the rate at which mutations arise in a bacterium that can lead to resistance to develop to an antimicrobial agent. "Mutation prevention concentration" or "MPC" refers to the lowest concentration of antimicrobial agent above which the selective proliferation of resistant mutants is expected to occur only rarely.Small Intestinal Bacterial Overgrowth

[0116] The devices and methods described herein can be used in the diagnosis and / or treatment of small intestinal bacterial overgrowth (SIBO) in a subject. In some embodiments, a subject having or presenting symptoms of SIBO can be diagnosed and / or a course of treatment can be determined for the subject using the methods described herein. The course of treatment comprises orally administering an effective amount of a pharmaceutical formulation comprising an antimicrobial agent to a subject, thereby treating SIBO in the subject.

[0117] A "symptom" or "symptomology" of SIBO refers to any morbid phenomenon or departure from the normal in structure, function, or sensation, experienced by a subject and indicative of disease. Exemplary symptoms include, but are not limited to, abdominal pain, abdominal cramps, abdominal discomfort, bloating, flatulence, distension, disturbed bowel function (e.g., constipation, diarrhea, or mixed constipation and diarrhea), excessive mucous in stool, slow bowel transit, nausea, and upper gastrointestinal symptoms (e.g., dyspepsia, heartburn, nausea, or vomiting), poor appetite, blood in stool (e.g., hematochezia or melena), weight loss, fever, abdominal tenderness, gastric stasis, and steatorrhea.

[0118] In some embodiments, SIBO presents chronic or semichronic symptomology. In some embodiments, SIBO presents acute symptomology. In some embodiments, the symptoms of SIBO have a temporal duration of about 12 hours, 24 hours, 36 hours, 48 hours, 72 hours, 84 hours, 96 hours, or more. In some embodiments, the symptoms of SIBO have a temporal duration of about 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days (i.e., 1 week), 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, or more. In some embodiments, the symptoms of SIBO have a temporal duration of about 1 month, 2 months, 3 months, 4 months, 5 months, or more. In some embodiments, the symptoms of SIBO have a temporal duration ≥ 6 months (e.g., 6 months, 7 months, 8 months, 9 months, 12 months, 1 year, 2 years, 3 years, or more).

[0119] The methods and devices described herein can be used to diagnose, treat and / or monitor subjects having or presenting symptoms of SIBO.

[0120] The subject has or is presenting symptoms of small intestinal bacterial overgrowth (SIBO). The small intestine houses less than 10 3< bacteria / mL under healthy conditions. When the homeostasis of the gut microbiome is disrupted or aberrant, various functions of the gut microbiota are uncontrolled. See, e.g., Shreiner et al. (2016) Curr. Opin. Gastroenterol. 31(1):69-75; Bures et al. (2010) World J. Gastroenterol. 16(24):2978-2990; and Adike and DiBaise (2018) Gastroenterol. Clin. North Am. 47(1):193-208. Excessive levels of bacteria and / or archaea (e.g., over 10 5< bacteria / mL) and abnormal types of bacteria and / or archaea in the small intestine may lead to the development of SIBO. SIBO is associated with chronic diarrhea, abdominal discomfort, bloating, malabsorption, flatulence, and unintentional weight loss. While Gram-positive bacteria are typically found in the small intestine, subjects suffering from SIBO have a variety of bacteria in the small intestine including Gram-negative bacteria, which are normally only present in very small numbers or not at all within the small intestine. For example, bacteria present in SIBO may secrete mucosal damaging toxins or metabolize bile salts, which can lead to malabsorption and bloating. A study comparing the prevalence of SIBO in subjects aged 24 to 50 and in subjects aged 61 or older found that SIBO was more prevalent in older subjects as compared to younger subjects (15.6% and 5.9% respectively) (Parlesak et al. (2003) J. Am. Geriatr. Soc. 51(6):768-773). SIBO was also seen more frequently in subjects with reduced body weight. Risk factors for developing SIBO include: metabolic disorders (e.g., diabetes, hypochloryhydria), malnutrition, irritable bowel syndrome (IBS), Celiac disease, Crohn's disease, cirrhosis, renal failure, gastroparesis, small bowel dysmotility, structural abnormalities of the GI tract (e.g., jejunal diverticula), gastric resection and immuno-deficiency. Additional risk factors include the use of certain medications (e.g., antibiotics, gastric acid secretion inhibitors). See, e.g., Dukowicz et al. (2007) Gastroenterol. Hepatol. 3(2):112-122. In some embodiments, subjects having SIBO have delayed intestinal transit times (Cuoco et al. (2002) Hepatogastroenterology 49:1582-1586). In some embodiments, subjects having SIBO have accelerated intestinal transit times (Van Citters and Lin (2006) Clin. Nutrition in Gastrointestinal Disease. Thorofare: Slack Inc; 2006; 271-280).

[0121] As used herein, a subject has or is at risk of having SIBO if the subject has intestinal bacteria and / or archaea levels that are greater than 10 3< colony forming units (CFU) / mL, e.g., greater than 10 4< CFU / mL, greater than 10 5< CFU / mL, greater than 10 6< CFU / mL, greater than 10 7< CFU / mL, greater than 10 8< CFU / mL, greater than 10 9< CFU / mL, greater than 10 10< CFU / mL. In some embodiments, the bacteria are both Gram-positive and Gram-negative bacteria. In some embodiments, the bacteria are Gram-positive bacteria. In some embodiments, the bacteria are Gram-negative bacteria. In some embodiments, the archaea are methane-producing (i.e., methanogenic) archaea.

[0122] The prevalence of SIBO in healthy individuals varies from about 0-20% (see, e.g., Lombardo et at. (2010) Clin. Gastroenterol. Hepatol. 8:504-8; Sabaté et al. (2008) Obes. Surg. 18:371-7; Posserud et al. (2007) Gut 56:802-8; Teo (2004) J. Gastroenterol. Hepatol. 19:904-9; Lewis et al. (1999) Age Ageing 28:181-5; Pimentel et al. (2003) Am. J. Gastroenterol. 98:412-9; Rana et al. (2011) Diabetes Technol. Ther. 13:1115-20; Bratten et al. (2008) Am. J. Gastroenterol. 103:958-63; and Scarpellini et al. (2009) J. Pediatr. 155:416-20).

[0123] Several clinical conditions are associated with SIBO and are referred to herein as "SIBO-related conditions." Exemplary SIBO-related conditions include, but are not limited to, coeliac disease (see, e.g., Rana et al. (2007) Trop. Gastroenterol. 28:159-61; Rubio-Tapia et al. (2009) J. Clin. Gastroenterol. 43:157-61; and Tursi et al. (2003) Am. J. Gastroenterol. 98:839-43), connective tissue diseases such as scleroderma (see, e.g., Levesque et al. (2009) Rheumatology 48:1314-9; and Parodi et al. (2008) Am. J. Gastroenterol. 103:1257-62), Crohn's disease (see, e.g., Fukushima et al. (1999) Dis. Colon Rectum 42:1072-7; Klaus et al. (2009) Gastroenterol. 9:61; and U.S. Publication No. 2002 / 0039599), diabetes mellitus (see, e.g., Rana et al. (2011) Diabetes Technol Ther 13:1115-20, and Zaccardi et al. (2009) Eur. Rev. Med. Pharmacol. Sci. 13:419-23), hypothyroidism (see, e.g., Lauritano et al. (2007) J. Clin. Endocr. Metab. 92:4180-4), nonspecific dysmotility (see, e.g., Jacobs et al. (2013) Aliment. Pharmacol. Ther. 37:1103-11), radiation enteropathy (see, e.g., Wedlake et al. (2008) Eur. J Cancer 44:2212-7), ulcerative colitis (see, e.g., Ibanez et al. (2008) Gastroenterology 134:A-350), chronic fatigue syndrome (see, e.g., Ojetti et al. (2009) Eur. Rev. Med. Pharmacol. Sci. 13:419-23), chronic pancreatitis (see, e.g., Mancilla et al. (2008) 136:976-80; and Trespi et al (1999) Curr. Med. Res. Opin. 15:47-52), drug-induced inhibition of acid secretion (see, e.g., Jacobs (2013) Aliment. Pharmacol. Ther. 37:1103-11; Compare et al. (2010) Eur. J. Clin. Invest. 41:380-6; and Lombardo et al. (2010) Clin. Gastroenterol. Hepatol. 8:504-8), end-stage renal failure (see, e.g., Strid et al. (2003) Digestion 67:129-37), fibromyalgia (see, e.g., U.S. Publication No. 2002 / 0039599), irritable bowel syndrome (Posserud et al. (2007) Gut 56:802-8; Bratten et al. (2008) Am. J. Gastroenterol. 103:958-63; 30. Pimentel et al. (2000) Am. J. Gastroenterol. 95:3503-6; Nucera et al. (2005) Aliment. Pharmacol. Ther. 21:1391-5; Lupascu et al. (2005) Aliment. Pharmacol. Ther. 22:1157-60; and Grover et al. (2008) Neurogastroenterol. Motil. 20:998-1008), immunodeficiency syndromes such as HIV- infection and chronic lymphocytic leukaemia (see, e.g., Chave et al. Am. J. Gastroenterol. 89:2168-71; and Smith et al. (1990) J. Clin. Pathol. 43:57-9), liver cirrhosis (see, e.g., Yang et al. (1998) Scand. J. Gastroenterol. 33:867-71; and Gunnarsdottir (2003) Am. J. Gastroenterol. 98:1362-70), obesity (see, e.g., Sabaté et al. (2008) Obes. Surg. 18:371-7; and Madrid et al. (2011) Dig. Dis. Sci. 56:155-60), parenteral nutrition (see, e.g., Gutierrez et al. (2012) J. Pediatr. Surg. 47:1150-4), rosacea (Parodi et al. Clin. Gastroenterol. Hepatol. 6:759-64), muscular dystrophy (see, e.g., Tarnopolsky et al. (2010) Muscle Nerve 42:853-5), and Parkinson's disease (see, e.g., Gabrielli (2011) Movement Disord. 26:889-92), and coronary artery disease (CAD) (Fialho et al. (2018) Dig. Dis. Sci. 63(2):412-421). In a recent study, CAD was significantly more prevalent in patients with SIBO as compared to those without SIBO (78.9% vs. 38.6%, P < 0.001) (Fialho et al. (2018)). Moreover, an increased numbers of vessels were affected by CAD among patients with SIBO as compared to those without SIBO. The mechanism by which SIBO is associated with CAD is unknown. Without wishing to be bound by any particular theory, SIBO may contribute to CAD through an increased production of bacterial byproducts such as lipopolysaccharide (LPS) and trimethylamine-N-oxide (TMAO) due to the high bacterial burden in the gut, which may induce a highly inflammatory and proatherogenic state. Microbes convert dietary nutrients that possess a TMA moiety (such as choline, phosphatidylcholine, ybutyrobetaine (yBB), and L-carnitine) into TMAO using specific microbial enzymes (e.g., TMA lyase) via a several metabolic pathways (see Tang and Hazen (2014) J. Clin. Invest. 124:4204-11). TMA is absorbed by the host subject, converted to TMAO by hepatic flavin monooxygenase 3 (FMO3), and excreted by the kidneys. In some embodiments of any of the methods described herein, one or more analytes including TMA, TMAO, carnitine, and ybutyrobetaine are measured in the GI tract of the subject (either in vivo using an ingestible device described herein or ex vivo in a sample obtained from the GI tract of the subject using an ingestible device described herein). Assays for measuring TMA, TMAO, carnitine, and ybutyrobetaine are known in the art.

[0124] In some embodiments of any of the methods described herein, a subject identified as having SIBO is further screened to determine whether the subject has or is at risk of developing a cardiovascular disease. Methods for detecting cardiovascular disease or a risk of developing cardiovascular disease in a subject are known in the art and include, for example, blood pressure, blood tests including a lipid profile, high density cholesterol, low density, cholesterol, triglycerides, cardiac biomarkers (enzymes, proteins, and hormones, such as troponin, myoglobin, b-type natriuretic peptide and creatine phosphokinase, that are associated with heart function, damage or failure), electrocardiograms (ECG or EKG), stress tests, chest x-ray, MUGA scan, computed tomography (CT), nuclear scanning (nuclear heart scan), echocardiogram (heart ultrasound), cardiac catheterization (coronary angiography), duplex / doppler ultrasound, magnetic resonance angiography (MRA) and magnetic resonance imaging (MRI) (see e.g., U.S. Patent Publication No. US 2006 / 0051873).

[0125] Thus, in some embodiments of any of the methods described herein, the subject has or is presenting symptoms of a SIBO-related condition selected from the group consisting of coeliac disease, a connective tissue disease (e.g., scleroderma), Crohn's disease, diabetes mellitus, hypothyroidism, nonspecific dysmotility, radiation enteropathy, ulcerative colitis, chronic fatigue syndrome, chronic pancreatitis, drug-induced inhibition of acid secretion, end-stage renal failure, fibromyalgia, irritable bowel syndrome, an immunodeficiency syndrome (e.g., HIV-infection and chronic lymphocytic leukaemia), obesity, parenteral nutrition, rosacea, muscular dystrophy, Parkinson's disease, and coronary artery disease.

[0126] In some embodiments, the SIBO-related condition is an autoimmune disease.

[0127] In some embodiments, the SIBO-related condition is selected from the group consisting of irritable bowel syndrome, fibromyalgia, chronic fatigue syndrome, depression; attention deficit / hyperactivity disorder, multiple sclerosis, systemic lupus erythematosus, and Crohn's disease.

[0128] In some embodiments, the SIBO-related condition is hyperalgesia.

[0129] The skilled medical practitioner is aware of suitable up-to-date diagnostic criteria by which a diagnosis for any of the SIBO-related conditions is made. These diagnostic criteria are based on a presentation of symptom(s) by a human subject. For example, these criteria include, but are not limited to, the Rome criteria for IBS (W. G. Thompson, Lancet 341:1569-72 (1993)) and the criteria for CFS established by the Centers for Disease Control and Prevention (CDC). (K. Fukuda et al., Ann. Intern. Med. 121:953-59 (1994)). The diagnostic criteria for fibromyalgia of the American College of Rheumatology will also be familiar (F. Wolfe et al., Arthritis Rheum. 33:160-72 (1990)), as will be the criteria for depression or ADHD provided for example, by the Diagnostic and Statistical Manual (DSM)-IV or its current version. (e.g., G. Tripp et al., J. Am. Acad. Child Adolesc. Psychiatry 38(2):156-64 (1999)). Symptoms of systemic lupus erythematosus include the 11 revised criteria of the American College of Rheumatology, such as a typical malar or discoid rash, photosensitivity, oral ulcers, arthritis, serositis, or disorders of blood, kidney or nervous system. (E. M Tan et al., Arthritis Rheum. 25:1271-77 (1982)). Appropriate diagnostic criteria for multiple sclerosis are also familiar (e.g., L. A. Rolak, Neuronal Clin. 14(1):27-43 (1996)), as are symptoms of Crohn's disease useful in reaching a suspected diagnosis. (e.g., J. M. Bozdech and R. G. Farmer, Hepatogastroenterol. 37(1):8-17 (1990); M. Tanaka and R. H. Riddell, Hepatogastroenterol. 37(1):18-31 (1990); A. B. Price and B. C. Morson, Hum. Pathol. 6(1):7-29 (1975)). The practitioner is, of course not limited to these illustrative examples for diagnostic criteria, but should use criteria that are current.

[0130] The methods described herein may be used to detect SIBO in a subject having a SIBO-related condition.

[0131] In some embodiment of any of the methods described herein, the subject is suspected of having SIBO or a SIBO-related condition. In some embodiments of any of the methods described herein, the subject has one or more symptoms selected from the group consisting of bloating, diarrhea, flatulence, stool frequency, abdominal pain, constipation, weight loss, fever, abdominal tenderness, nausea, gastric stasis, and steatorrhea.

[0132] In some embodiments of any of the methods described herein, the subject has been subjected to a surgical intervention. For example, SIBO is prevalent in subjects that have undergone abdominal surgery, bilateral vagotomy, gastrectomy, ileocaecal valve resection, and roux-en-Y reconstruction (see, e.g., Grace et al. (2013) Aliment. Pharmacol. Ther. 38(7):674-88). In some embodiment of any of the methods described herein, the subject has been subjected to a surgical intervention selected from the group consisting of abdominal surgery, bilateral vagotomy, gastrectomy, ileocaecal valve resection, and roux-en-Y reconstruction.

[0133] In some embodiments of any of the methods described herein, the subject has a GID associated with anomalous bacterial and / or archaeal populations. The bacteria may include, but are not limited to, the types of bacteria and / or archaea present in the fluid sample or the concentration of bacteria and / or archaea in specific regions of the GI tract. Data obtained using the methods described herein may be used to determine whether a subject has an infection, such as small intestinal bacterial overgrowth (SIBO), or to characterize bacterial and / or archaeal populations within the GI tract for diagnostic or other purposes.

[0134] In some embodiments, the methods described herein can be used to determine whether a subject has an elevated level of one or more bacterial species and / or strains associated with SIBO in a fluid obtained from the small intestine (e.g., jejunum) of the subject. Bacteria associated with SIBO include, but are not limited to, bacteria of the following genera: Actinobacillus, Actinomyces, Bacteroides, Campylobacter, Citrobacter, Clostridium, Corynebacterium, Escherichia, Enterobacter, Enterococcus, Fusobacterium, Gemella, Granulicatella, Haemophilus, Klebsiella, Lactobacillus, Lachnoclostridium, Leptotrichia, Megasphaera, Neisseria, Oribacterium, Parascardovia, Porphyromonas, Prevotella, Proteus, Pseudomonas, Ralstonia, Rothia, Staphylococcus, Streptococcus, and Veillonella. Exemplary species of bacterial species associated with SIBO include Bacteroides fragilis, Bacteroides distasonis, Bacteroides melanogenicus, Bacteroides ovatus, Bacteroides thetaiotamicron, Bacteroides uniformis, Bacteroides urolyticus, Bacteroides vulgatus, Citrobacter diversus, Citrobacter freundii, Citrobacter koseri, Escherichia coli, Enterobacter aerogenes, Klebsiella pneumoniae, Staphylococcus aureus, Prevotella bivia, Prevotella intermedia, Prevotella melanogenica, Proteus mirabilis, Pseudomonas aeruginosa, Haemophilus influenzae, Haemophilus parainfluenzae, Streptococcus agalactiae, Streptococcus mutans, Streptococcus pneumoniae, Streptococcus pyogenes, Enterococcus faecalis, and Clostridium sporogenes. Thus, in some embodiments of the methods described herein, elevated levels of one or more (for example, two or more, three or more, four or more, five or more) bacterial species and / or strains associated with SIBO (either alone or in combination) indicates that a subject has or is at risk of developing SIBO.

[0135] In some embodiments, an elevated level of one or more bacterial species and / or strains associated with SIBO is greater than about 10 3< colony forming units (CFU) / mL, e.g., greater than about 10 4< CFU / mL, greater than about 10 5< CFU / mL, greater than about 10 6< CFU / mL, greater than about 10 7< CFU / mL, greater than about 10 8< CFU / mL, greater than about 10 9< CFU / mL, or greater than about 10 10< CFU / mL.

[0136] In other embodiments, the devices and methods described herein are used to identify, characterize and / or quantify bacteria in the GI tract of a subject (e.g., in vivo or ex vivo) associated with SIBO. In some embodiments, the relative abundance of Proteobacteria phylum and Firmicutes phylum is determined using the devices and methods described herein, wherein a Firmicutes / Proteobacteria ratio (F / P) is lower in SIBO vs. non-SIBO subjects. In another embodiment, bacterial analysis (e.g., characterization or quantification) is done on a sample from the duodenum or the proximal jejunum.

[0137] In other embodiments, the devices and methods described herein are used to identify, characterize and / or quantify bacteria in the GI tract of a subject (e.g., in vivo or ex vivo) associated with IBD. For example, Proteus, a Gram-negative facultative anaerobic bacilli, has been identified as a key genus in Crohn's disease (CD) recurrence after intestinal resection. Thus, in some embodiments, the relative abundance of Proteus, particularly those belonging to the P. mirabilis lineages, is determined using the devices and methods described herein, wherein a higher abundance of Proteus is seen in CD patients compared to healthy controls.

[0138] In yet other embodiments, the devices and methods described herein are used to identify, characterize and / or quantify bacteria in the GI tract of a subject (e.g., in vivo or ex vivo) associated with microscopic colitis. For example, global and Alistipesfinegoldii-specific peak-to-trough ratios (PTRs) are significantly higher in active microscopic colitis compared to healthy controls. In multivariable analyses, Haemophilus parainfluenzae, Veillonella parvula, and Veillonella unclassified species are more abundant in microscopic colitis than healthy controls, while Alistipes putredinis are less abundant in active microscopic colitis patients. Thus, in some embodiments, the global and Alistipesfinegoldii-specific peak-to-trough ratios (PTRs) are determined using the devices and methods described herein, wherein higher PTRs are seen in active microscopic colitis compared to healthy controls. In other embodiments, the relative abundance of Haemophilus parainfluenzae, Veillonella parvula, and Veillonella unclassified species are determined using the devices and methods described herein, wherein a higher abundance of Haemophilus parainfluenzae, Veillonella parvula, and Veillonella unclassified species are seen in active microscopic colitis compared to healthy controls.

[0139] Elevated levels of methane have been observed in subjects having SIBO (referred to as "methane-dominant SIBO" or "methane-predominant SIBO") and other GI disorders such as IBS (see, e.g., Low et al. (2010) J. Clin. Gastroenterol. 44(8):547-50; Goettlieb et al. (2016) Aliment Pharmacol Ther.43(2):197-212; and Adike and DiBaise (2018) Gastroenterol. Clin. North Am. 47(1):193-208). In some embodiments, the methods described herein may be used to determine the concentration of methane in the GI tract of a subject having SIBO using an ingestible device described herein. In some embodiments, the methods described herein may be used to determine whether a subject has an elevated level of one or more methanogenic archaeal species and / or strains associated with methane-dominant SIBO (e.g., Methanobrevibacter smithii) in a sample obtained from the gastrointestinal intestinal tract (e.g., jejunum) of the subject. In some embodiments, an elevated level of one or more methanogenic archaeal species and / or strains associated with SIBO is greater than about 10 3< colony forming units (CFU) / mL, e.g., greater than about 10 4< CFU / mL, greater than about 10 5< CFU / mL, greater than about 10 6< CFU / mL, greater than about 10 7< CFU / mL, greater than about 10 8< CFU / mL, greater than about 10 9< CFU / mL, or greater than about 10 10< CFU / mL. Subjects identified as having elevated levels of methane or elevated levels of methanogenic archaea can be treated with an antimicrobial agent that is effective against methanogenic archaea. In some embodiments, the subject can be administered a pharmaceutical formulation comprising at least one antibiotic described herein. Exemplary antibiotics effective against methanogenic archaea include, but are not limited to, lovastatin (e.g., lovastatin lactone), neomycin, rifaximin, and combinations thereof.Methods of Diagnosing and Treating a Subject Having SIBO

[0140] In some embodiments, the methods described herein include performing one or more assays to determine and / or identify whether a subject having SIBO symptomology has or is at risk of developing SIBO. The assays allow for a skilled practitioner (e.g., a physician) to screen the subject in order to assess the GI tract function of the subject, and the presence and absence of one or more biomarkers associated with SIBO, to accurately diagnose the subject and / or provide an adequate treatment. For example, the assays / tests described herein will allow a skilled practitioner to diagnose a subject presenting with SIBO symptomology based on the identification of specific biomarkers or functional characteristics.

[0141] One or more of these assays / tests may be performed before, concurrently, or after commencing an intervention. In some embodiments, one or more of the assays / tests are performed using a sample that has been obtained from the subject (e.g., a fecal, tissue, or blood sample) from the subject. In some embodiments, the subject is administered an ingestible device described herein to obtain a sample from the subject and the assay is performed ex vivo. In some embodiments, the subject is administered an ingestible device described herein to obtain a sample from the subject and the assay is performed in vivo. In some embodiments, a sample is obtained from the subject without using an ingestible device described herein. In some embodiments, one or more additional tests is performed to screen the subject, including, for example, a colonoscopy, an endoscopy, an abdominal / pelvic CT scan, a colonic transit test, anorectal monometry, pelvic floor function test, rectal sensation and emptying test, defecography, a breath test to detect methane levels, esophageal manometry, gastric emptying, or anorectal manometry.Intestinal Barrier Function

[0142] In some embodiments, the methods described herein include performing an assay to determine the gastrointestinal barrier function of a subject. The intestinal barrier is a complex system that protects against intestinal luminal content which includes enteric flora, antigens and toxins, while permitting the absorption of nutrients, electrolytes, and water. As used herein, the term "intestinal barrier" refers to the functional system that separates the gut lumen from the subject's internal milieu, and includes mechanical components (e.g., mucus and the epithelial layer), immunological components (e.g., defensins, IgA, lymphocytes, and innate immune cells), muscular components, and neurological components. A defective intestinal barrier may result in increased intestinal permeability, thereby allowing for exposition of luminal content and the triggering of immunological responses that promote intestinal inflammation. Many factors can alter intestinal permeability including gut microbiota changes, mucus layer alterations, and epithelial damage, as well as the consumption of alcohol and energy-dense food (Bischoff et al. (2014) BMC Gastroenterol. 14:189). Generally, altered intestinal barrier function resulting in intestinal permeability is associated with inflammation. For example, altered intestinal permeability has been reported in patients having irritable bowel syndrome, steatoheptatitis, acute pancreatitis, multiple organ failure, major surgery, and trauma (Michielan and D'Inca (2015) Mediators Inflamm. 2015:628157). In addition, altered intestinal permeability plays an important role in the pathogenesis of intestinal inflammation and in the severity of several GFIDs including IBD, Crohn's disease, and ulcerative colitis (see, e.g., Antoni et al. (2014) World J. Gastroenterol. 20(5):1165-79). Altered intestinal barrier function may also be caused by intestinal infection, ingestion of allergenic foods or toxic compounds, deficient secretory IgA, trauma, endotoxemia, and nonsteroidal anti-inflammatory drugs (NSAIDs).

[0143] Multiple assays for determining intestinal barrier function are known in the art and are described, for example, in PCT Publication Nos. WO2014 / 039699, WO2016 / 036887A1, WO2017 / 136511A1, and WO2017 / 173203A1; Bischoff et al. (2014) BMC Gastroenterol. 14:189; and Kelly et al. (2015) Front Cell. Neurosci. 9:392. For example, intestinal barrier function may be measured by assessing biomarkers of epithelial integrity such as soluble adhesion molecules, immunological biomarkers, inflammation biomarkers, or bacterial markers such as circulating endotoxin. In addition, histological and microscopic analyses can be performed to assess intestinal permeability.

[0144] In some embodiments, the intestinal barrier function of a subject is determined using a lactulose / mannitol (L / M) test. The L / M test evaluates small intestinal permeability by measuring the urinary excretion of lactulose and mannitol after oral administration. Lactulose is a large disaccharide that only partially absorbed by a healthy gut but it absorption is increased when a subject exhibits decreased intestinal barrier function. Mannitol is a smaller monosaccharide that is easily absorbed since it freely crosses the intestinal epithelium. To perform the test, a subject is orally administered a solution containing both mannitol and lactulose, urine samples are collected over a 24-hour period, and samples are analyzed to detect sugar levels (e.g., using liquid chromatography-tandem mass spectrometry). The analysis of urine samples collected at different time points following administration is used to estimate permeability along the gastrointestinal tract. For example, sugar excretion measured in urine samples collected between 0-2 hours after administration of the reflects small intestine and colon permeability, while sugar excretion in urine samples collected between 6 and 24 hours after administration reflect colonic permeability (see, e.g., Camilleri et al. (2010) Neurogastroenterol. Motil. 22(1):e15-e26). High levels of both sugars in the urine samples is indicative of altered barrier function (e.g., leaky gut syndrome). Low levels of both sugars indicates malabsorption of nutrients by the subject. High levels of mannitol and low levels of lactulose in the samples indicate that the subject has normal intestinal barrier function.

[0145] In addition to the dual-sugar M / N test, a multi-sugar assay can be used to determine intestinal barrier function as described, for example, in van Wijck et al. (2013) Clin. Nutr. 32(2):245-51. Intestinal barrier function can also be assessed by measuring the absorption and excretion of polyethylene glycols (PEGs) (see, e.g., Bjarnason et al. (1995) Gastroenterology 108:1566-81). Like sugars, large molecular weight PEGs (400-4000 Da) will only cross the intestinal mucosa when intestinal barrier integrity is compromised. Urinary levels of large molecular weight PEGs can be measured using gas chromatography or high pressure liquid chromatography (HPLC) after oral administration to a subject (e.g., 24 hours post-administration). Increased urinary levels of high molecular weight PEGs is indicative of decreased barrier function (and intestinal permeability) (see, e.g., Grootjans et al. (2010) World J. Gastrointest. Surg. 2:61-69.

[0146] In some embodiments, intestinal barrier function can be assessed using a functional test such as the 51< Cr-EDTA test (see, e.g., Jenkins et al. (1988) Clin. Invest. Med. 11(2):151-5). 51< Cr-EDTA is easily detectable, has similar physiological properties to oligosaccharides, and is not degraded by the bacterial flora of the colon. In this test, a subject is administered 51< Cr-EDTA, and the excretion of the molecule is monitored in urine samples from the subject. In a healthy gut, 51< Cr-EDTA cannot cross the intestinal epithelia and therefore only minimal levels of the 51< Cr-EDTA penetrate the circulation and can be detected in urine. However, if intestinal barrier function is disrupted, higher levels of 51< Cr-EDTA are detected in urine.

[0147] Intestinal barrier function may also be assessed using passive measurements. When intestinal barrier function is compromised, bacteria and bacterial products can be found in the circulation of the subject (e.g., in plasma or serum). In some embodiments, the intestinal barrier function of a subject is assessed by measuring plasma endotoxin (e.g., LPS and / or lipoglycan) levels. Endotoxin is a lipopolysaccharide present in the outer membrane of Gran-negative bacteria. The limulus amebocyte lysate assay (LAL assay) can be used to measure plasma endotoxin levels. LAL is derived from extracts of primitive amebocytes from horseshoe crab. The lipid A component of endotoxin interacts with pro-clotting enzymes in LAL activating a cascade that results in gelation and clot formation. Two common variations of the LAL assay, the turbidometric LAL assay and the chromogenic LAL assay, are commercially available (Endosafe KTA2 lysate (Charles River Laboratories, France); Endochrome-K lysate (Charles River Laboratories, France); QCL-1000 kit; Lonza, Walkersville, MD, USA). Alternatively, plasma or serum endotoxin can be measured using reverse phase HPLC / MS / MS as described in Pais de Barros et al. (2015) J. Lipid Res. 56(7):1363-9.

[0148] Intestinal barrier function may also be assessed by measuring the concentration of immunoglobulins (e.g., IgG, IgM, or IgA) against the inner core of endotoxin, also known as "endotoxin core antibodies" (EndoCAb), in the whole blood, plasma and / or serum of a subject. In some embodiments, the concentration of EndoCAb can be measured using an enzyme-linked immunosorbent assay (ELISA) (see, e.g. Bennett-Guerrero et al. (1999) JAMA 277(8):646-50; Hamilton-Davies et al. (1997) Chest 112(5):1189-1196, 1997; Barclay (1995) "Endogenous Endotoxin-Core Antibody (EndoCAb) as a Marker of Endotoxin Exposure: A Review," In Levin et al., eds., "Bacterial Endotoxins: Lipopolysaccharides From Genes to Therapy," New York, NY, Wiley-Liss, 263-272; Barclay et al. (1987) Infect. Immun. 55:2706-14; and U.S. Patent Publication No. US 2003 / 0190313 A1). Immunoassay kits for the detection of EndoCAb are commercially available (DiaPharma EndoCAb kit, DiaPharma Group, Inc., West Chester, Ohio, USA; HBT Endocab test kit HK504, Canton, MA, USA).

[0149] Intestinal barrier function may be assessed by measuring the plasma levels of D-lactate. D-lactate is a fermentation product produced by many intestinal bacteria. In healthy subjects, circulating levels of D-lactate are low; however, when intestinal barrier function is compromised, increased circulating levels of D-lactate may be observed as a consequence of increased translocation of the compound across the intestinal barrier. Levels of D-lactate can be measured using a coupled enzymatic reaction utilizing D-lactate dehydrogenase and alanine aminotransferase, and measuring the formation of NADH as described in Fürst and Schiesser (1999) Anal Biochem. 269:214-5. Additional methods for analyzing plasma D-lactate levels have been described, for example, in Herrera et al. (2008) Ann. Clin. Biochem. 45(Pt. 2):177-83.

[0150] Intestinal barrier function of a subject may also be assessed using imaging techniques such as confocal laser endomicroscopy. Confocal laser endomicroscopy allows for the evaluation of gastrointestinal epithelial lining and vasculature using a molecular contrast agent (e.g., fluorescein) (see, e.g., Becker et al. (2008) Gastrointest. Endosc. 68(2):319-23; Kiesslich et al. (2007) Gastroenterol. 133(6):1769-78; and Liu et al. (2011) J. Clin. Gastroenterol. 45(3):240-5). In some embodiments, the intestinal barrier function of a subject is assessed by measuring autoantibody levels.Calprotectin

[0151] In some embodiments, the methods described herein include performing an assay to determine the concentration of calprotectin present in a fecal sample from a subject. Calprotectin (S100A8 / A9) is a calcium and zinc-binding protein generally found in the cytosol of human neutrophils and macrophages. During cell stress or damage, calprotectin can be detected in stool. Therefore calprotectin levels are considered sensitive marker of intestinal inflammation.

[0152] Although fecal calprotectin is elevated in subjects having inflammatory bowel disease (e.g., ulcerative colitis and Crohn's disease), it is not a specific marker for IBD. Any inflammatory process within the gastrointestinal tract results in the activation of the innate immune response and calprotectin release (Smith and Gaya (2012) World J Gastroenterol. 18(46):6782-9 and Poullis et al. (2003) J. Gastroenterol. Hepatol. 18:756-762). Fecal calprotectin levels are useful in detecting active IBD and predicting recurrence of disease (see Angriman et al. (2007) Clin. Chim. Acta 381:63-8). Calprotectin is very suitable as a biomarker of inflammation since it is generally resistant to bacterial degradation in the gut, and is stable in stool samples at room temperature for about one week. Fecal calprotectin can be detected by methods known in the art, including the PhiCal ®< Fecal Calprotectin Immunoassay (Genova Diagnostics, Inc., Asheville, NC, USA; Calpro AS, Oslo, Norway) which has been approved in the U.S.A. for use in diagnosing IBD. Additional human calprotectin detection kits are also commercially available including IDK ®< Calprotectin ELISA, Immunodianostik AG, Bensheim, Germany; and Human Calprotectin ELISA Kit, Cell Sciences ®< , Canton, Mass., USA.

[0153] Fecal calprotectin levels may be analyzed by using the PhiCal ®< Fecal Calprotectin Immunoassay, as instructed by the manufacturer. Calprotectin levels below about 50 µg per gram of stool are indicative of no inflammation in the GI tract. Fecal calprotectin levels between about 50 to about 120 µg / g stool are associated with low-grade inflammation, which may be caused by post-infectious irritable bowel syndrome (IBS), infection, food allergies, polyps, neoplasia, non-steroidal anti-inflammatory drugs (NSAIDs) or IBD in remission. Fecal calprotectin levels above about 120 µg / g stool indicates significant inflammation which may be caused by IBD, infection, food allergies, NSAID use, polyps, adenomas, colorectal cancer, or diverticulitis. Fecal calprotectin levels greater than about 250 µg / g stool indicate a strong likelihood that the subject has active IBD or is at a high risk of relapse to active IBD within one year. In subjects that have been diagnosed with IBD, fecal calprotectin levels between 250-500 µg / g stool indicates low to moderate disease activity, and fecal calprotectin levels above 500 µg / g stool suggest high disease activity. Subjects with IBD in remission and fecal calprotectin levels above 250 µg / g stool have a high risk of relapse within one year.C-reactive protein (CRP)

[0154] In some embodiments, the methods described herein include performing an assay to determine the concentration of C-reactive protein present in a sample (e.g., blood, serum or plasma) from a subject. CRP (C-reactive protein) is an acute inflammatory protein biomarker that dramatically increases (up to 1,000-fold) at sites of inflammation or infection. Thus, in some embodiments, CRP levels may be used to determine whether a subject has inflammation. In some embodiments, CRP levels may be used to determine whether a subject has an infection. The protein is produced as a homopentameric protein referred to as native CRP (nCRP), but can dissociate into five monomers, called monomeric CRP (mCRP) (Sproston and Ashworth (2018) Front. Immunol. 9:754. Healthy subjects have low levels of CRP in circulation (less than 1 mg / L) but levels can rise 100-fold (even reaching 300-400 mg / L) in periods of acute inflammation (Chang et al. (2015) World J. Gastroenterol. 21(40):11246-59.

[0155] CRP levels may be determined using a less sensitive standard immunoassay (e.g., ELISA) that is useful for monitoring general inflammatory changes in patients where CRP levels are higher than 10 mg / L. Several of these immunoassays are commercially available including the Quantikine ®< human CRP Immunoassay kit (R&D Systems ®< , Minneapolis, MN, USA). A second type of detection assay referred to as a high sensitivity C-reactive protein test (hs-CRP) has a higher detection sensitivity and measures low levels of CRP. Blood or serum CRP levels less than 10 mg / L are typically tested using hs-CRP tests. Exemplary hs-CRP tests include the Cardio IQ ®< hs-CRP (Quest Diagnostics ®< , Seacacus, NJ, USA) CRP levels persistently above 10 mg / L may indicate an acute inflammatory process in a subject.7a-hydroxy-4-cholesten-3-one (7αC4)

[0156] In some embodiments, the methods described herein include performing an assay to determine the concentration of 7α-hydroxy-4-cholesten-3-one (7αC4) present in a sample (e.g., blood, serum or plasma) from a subject. The measurement of 7αC4 allows for the monitoring of the enzymatic activity of hepatic cholesterol 7α-hydroxylase, the rate limiting enzyme in the synthesis of bile acids and can be used as a surrogate to detect bile acid malabsorption (BAM) (see, e.g., Galman et al. (2003) J. Lipid. Res. 44:859-66; and Camilleri et al. (2009) Neurogastroeterol. Motil. 21(7):734-43).

[0157] Bile acids are products of cholesterol synthesis that are synthesized in the liver, conjugated to taurine or glycine, and stored in the gallbladder until released into the small intestine. The primary bile acids are cholic acid, and chenodeoxycholic acid, which are deconjugated and dehydroxylated by intestinal bacteria to form the secondary bile acids deoxycholic acid and lithocholic acid, respectively. The majority of bile acids (about 95%) are reabsorbed in the distal ileum and returned to the liver (see, e.g., U.S. Publication No. 2017 / 0343535). Impaired absorption of bile acids in the ileum can lead to excess bile acids in the colon which can cause symptoms of bile acid malabsorption (BAM; also known as bile acid diarrhea), including watery stool and fecal incontinence. Interestingly, up to 50% of patients with irritable bowel syndrome with diarrhea (IBS-D) also have BAM (see, e.g., Camilleri et al. (2009) Neurogastroeterol. Motil. 21(7):734-43).

[0158] In some embodiments, 7αC4 levels may be used to determine whether a subject has bile acid malabsorption. Serum 7αC4 concentration above about 65 ng / mL (e.g., above about 65.5 ng / mL, above about 66.0 ng / mL, above about 66.5 ng / mL, above about 67.0 ng / mL, above about 67.5 ng / mL, above about 68.0 ng / mL, above about 68.5 ng / mL, above about 69.0 ng / mL, above about 69.5 ng / mL, above about 70.0 ng / mL, above about 70.5 ng / mL, above about 71.0 ng / mL, above about 72.0 ng / mL, above about 73.0 ng / mL, above about 74.0 ng / mL, and above about 75.0 ng / mL) are indicative of bile acid malabsorption (see, e.g., Camilleri et al. (2009) Neurogastroenterol. Motil. 21(7):734-e43; and Sauter et al. (1999) Dig. Dis. Sci. 44(1):14-9). In some embodiments, the concentration of 7αC4 present in the blood, serum or plasma from the subject is analyzed using a high pressure liquid chromatography-tandem mass spectrometry (HPLC-MS / MS) assay as described in Camilleri et al. (2009) Neurogastroeterol. Motil. 21(7):734-43; or Honda et al. (2007) J. Lipid Res. 48(2):458-64. In some embodiments, subjects identified as having serum 7αC4 concentration above about 65 ng / mL indicates that the subject has bile acid malabsorption.

[0159] In some embodiments, the devices, methods and compositions described herein can be used to detect, quantitate, and / or analyze the presence and / or level of 7αC4 in the GI tract of a subject.Celiac Disease-Related Antibodies

[0160] In some embodiments, the methods described herein include performing a serological test (e.g., an ELISA) to detect and / or quantitate one or more of: anti-gliadin antibodies (AGA), anti-endomysial antibodies (EmA), anti-tissue transglutaminase antibodies (tTGA), anti-deamidated gliadin peptide antibodies (DGPA), and total serum IgA in a sample (e.g., blood, serum or plasma) from a subject. In some embodiments, AGA, EmA, tTGA, or DGPA are IgG antibodies (e.g., IgG AGA, IgG EmA, IgG tTGA, and IgG DGPA). In some embodiments, the AGA, EmA, tTGA, or DGPA are IgA antibodies (e.g., IgA AGA, IgA EmA, IgA tTGA, and IgA DGPA). AGA, EmA, tTGA, and DGPA are serological markers of Celiac disease. Thus, the detection and / or quantitation of these antibodies may be used to determine whether a subject has or is at risk of developing Celiac disease.

[0161] Serology assays are often used to diagnose Celiac disease in a subject (Dieterich et al. (1998) Gastroenterology 115:1317-21). Serology assays to detect IgA tTGA are considered the best strategy for Celiac disease serological screening as they are highly sensitive (up to 97%) (Volta and Villanacci (2011) Cell. Mol. Immunol. 8(2):96-102). Serology assays to detect IgA EmA are typically employed as confirmation tests in subjects that are positive for IgA tTGA due to their higher specificity (about 100 %, as compared to about 91% of the IgA tTGA assays) (Volta and Villanacci (2011)).

[0162] Serology assays to detect IgA AGA are recommended for the diagnosis of Celiac disease in young children (under 2 years of age) (Lagerqvist et al. (2008) J. Pediatr. Gastroenterol. Nutr. 47:428-35), while assays to detect IgG tTGA are recommended for detecting Celiac disease in subjects with an IgA deficiency (Cataldo et al. (1998) Gut 42:362-65).

[0163] Recently, serology assays to detect IgG and IgA DGPA have been developed. These assays have a lower sensitivity for Celiac disease than assays for IgA tTGA. Moreover, IgG DGPA serology assays show very high specificity for Celiac disease, and allow for the identification of the disease in most Celiac disease cases, including subjects having IgA-deficiency and children under 2 years of age (Volta et al. (2010) J. Clin. Gastroenterol. 44:186-19.

[0164] Kits for the detection and / or quantitation of IgG AGA, IgG EmA, IgG tTGA, IgG DGPA, IgA AGA, IgA EmA, IgA tTGA, and IgA DGPA are commercially available, for example from INOVA Diagnostics, San Diego, Calif. (see also, Prince (2006) Clin. Vaccine Immunol. 13(1):150-1; and U.S. Publication No. 2009 / 0176251 A1).GI Pathogen Screening

[0165] In some embodiments, the methods described herein include performing an assay to detect the presence or identity of a microorganism (e.g., a GI pathogen) in a sample from the subject (e.g., a fecal or blood sample). Any method known in the art may be used as described herein to assess whether a subject presenting a symptom of a GID has an infection with a GI pathogen (e.g., bacterial pathogens, protozoans, parasites, fungi, and viruses). Exemplary GI pathogens include, but are not limited to, a bacteria of one of the following genera: Staphylococci (e.g., Staphylococcus aureus), Shigella (e.g., Shigella dysenteriae, Shigella flexneri, Shigella boydii, and Shigella sonnei), Salmonella (e.g., Salmonella enterica and Salmonella bongori), Escherichia (e.g., Escherichia coli including enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC), or enterohemorrhagic E. coli (EHEC)), Vibrio (e.g., V. cholerae, V. vulnificus and V. parahemolyticus), Aeromonas (e.g., Aeromonas hydrophila), Plesiomonas (e.g., Plesiomonas shigelloides), Campylobacter (e.g., Campylobacter jejuni), Clostridium (e.g., Clostridium difficile), Helicobacter (e.g., Helicobacter pylori), Bacillus (e.g., Bacillus cereus), and Yersinia (e.g., Y. enterocolitica and Y. pseudotuberculosis); viruses, such as rotavirus A, norovirus GI / GII. and adenovirus 40 / 41; and parasites such as Cryptosporidium spp., Entamoeba histolytica and Giardia lamblia. For example, in some embodiments, the presence of a GI pathogen in a sample from the subject is detected using the xTAG ®< gastrointestinal pathogen panel (GPP) assay (Luminex Corporation, Austin, TX, USA; see also luminexcorp.com / clinical / infectious-disease / gastrointestinal-pathogen-panel / ). The GPP assay is a multiplexed nucleic acid test that detects up to 15 different pathogens that are responsible for gastroenteritis, including bacteria (Salmonella spp., Shigella spp., Vibrio cholerae, Yersinia enterocolitica, Campylobacter spp., Clostridium difficile, Escherichia coli 0157, Shiga toxin-producing E. coli and enterotoxigenic E. coli), viruses (rotavirus A, adenovirus 40 / 41 and norovirus GI / GII) and parasites (Cryptosporidium spp., Entamoeba histolytica and Giardia lamblia).

[0166] For example, traditional culture methods enable the identification and semi-quantitation of specific organisms through the utilization of differential growth media and solid plates, while microorganism classification and / or identification can be performed using Analytical Profile Index (API ®< ) strips (bioMerieux, Marcy l'Etoile, France; see also biomerieux-usa.com / clinical / api). This can also be accomplished using automated biochemical instruments such as Vitek. Other methods and techniques that can be used include mass spectrometry methods such as MALDI-TOF-MS (Matrix-assisted laser desorption / ionization time-of-flight mass spectrometry), which uses species- and strain-specific biomarkers to identify organisms. Microarray technology can also be used to evaluate nucleic acids, such as 16s rRNA, small peptides or molecules, such as toxins, that are specific for the microorganism, or carbohydrate (e.g., polysaccharide) profiles. Nucleic acid probe technology can also be used in combination with fluorescent microscopy for microbial quantification and identification. Other methods for identifying GI pathogens include nucleic acid amplification by PCR and RNA or DNA sequencing.

[0167] For example, Sanger sequencing or next generation sequencing (NGS) can be used to perform rapid microbial identification using 16S-23S rRNA regions or internal transcribed spacer regions (ITS) or whole genome sequencing (e.g., shotgun sequencing) can be performed (see, e.g., Deurenberg et al. (2017) J. Biotech. 243:16-24). Microorganisms can be identified through sequencing by identification of either segments of genetic material or the entire genome. In particular, ribosomal RNA (rRNA) sequences have been identified as a target for determining the phylogeny of an organism because it is present in all cells. Prokaryotic rRNA contains three main segments: 5S (~120 nt), 16S (~1.5 kb), and 23S (~2.9 kb). Bacterial identification can be achieved by sequencing the 16S small subunit (SSU) and 23S large subunit (LSU), which can be performed using either Sanger sequencing or next generation sequencing (see Sabat et al. (2017) Sci. Rep., 7(1), 3434). This enables identification of bacterial organisms based on sequencing these rRNA segments and comparing to existing rRNA databases, such as the Ribosomal Database Project (RDP-II) or SILVA (see, e.g., Cole et al. (2003). Nucleic Acids Res., 31(1):442-443; and Pruesse et al. (2007) Nucleic Acids Research 32(21):7188-96). The sequenced prokaryotic DNA or RNA can then be identified using pre-prepared libraries such as k-mer or BLAST (Deurenberg et al. (2017)). Various systems and products for the preparation of sample, sequencing, and analysis of genomic sequences derived from microbial organisms are commercially available including, for example, the Nextera ®< XT DNA Library Preparation Kit, the MiSeq ®< System and Reagent Kits, and the 16S Metagenomics software (all produced by Illumina ®< , Inc.) and the Ion PGM ™< (ThermoFischer) (see also Rapin et al. (2017) Curr. Protoc. Mouse Biol. 7(2):100-29).

[0168] Microbial whole genome sequencing is particularly advantageous as genes associated with resistance and / or virulence can be identified and used to predict antibiotic resistance, antibiotic susceptibility, and microbial virulence characteristics. Probes (e.g., oligonucleotides) specific for genes encoding genes associated with resistance and / or virulence of a microorganism can be used to identify and characterize microorganisms. Additional methods for identifying GI pathogens include competitive and non-competitive immunoassays, enzyme immunoassay (EIA), radioimmunoassay (RIA), antigen capture assays, two-antibody sandwich assays, Western blot analysis, enzyme linked immunosorbent assays (ELISAs), and the like. Staining techniques accompanied by microscopy may also be used (see, e.g., Garcia et al. (2017) Clin Microbiol Rev. 31(1):pii: e00025-17; McHardy et al. (2014) J. Clin. Microbiol. 52(3):712-20). Additional testing methods are described for example, in Drancourt et al. (2016) Clinical Microbiology Reviews 29(3):429-47.SIBO

[0169] In some embodiments, the methods described herein include performing an assay or test to determine whether a subject has SIBO. In some embodiments, a small intestine or jejunal aspirate is obtained from the subject (e.g., using a special sonde or via enteroscopy) and directly cultured. Sampling can be achieved by intubation followed by scrape, biopsy, or aspiration of the contents of the intestinal lumen, including the lumen of the duodenum, jejunum, or ileum. Further, any of the contents of the intestinal lumen including material of a cellular, fluid, fecal, or gaseous nature, or sampling is of the lumenal wall itself can be sampled. Analysis of the sample to detect bacterial overgrowth is by conventional microbiological techniques including microscopy, culturing, and / or cell numeration techniques. The detection of greater than about 1×10 3< CFU / mL, greater than about 1×10 4< CFU / mL, or greater than about 1×10 5< CFU / mL of fluid can be indicative of SIBO.

[0170] In some embodiments, an ingestible device described herein may be administered to a subject to determine if the subject has SIBO. For example, a device described herein may be used to detect the presence of bacterial growth in a dilution from a jejunal fluid sample, and a bacterial concentration of about 10 5< CFU / mL or greater in the jejunal fluid is indicative that the subject has SIBO.

[0171] Another exemplary method of detecting small intestinal bacterial overgrowth is by endoscopic visual inspection of the wall of the duodenum, jejunum, and / or ileum.

[0172] Breath hydrogen testing is another exemplary method of detecting SIBO in a patient (e.g., P. Kerlin and L. Wong, Gastroenterol. 95(4):982-88 (1988); A. Strocchi et al., Gastroenterol. 105(5):1404-1410 (1993); D. de Boissieu et al., (1996); P. J. Lewindon et al., J. Paedatr. Child Health 34(1):79-82 (1998)). Breath hydrogen (and breath methane) tests are based on the fact that many obligately or facultatively fermentative bacteria found in the gastrointestinal tract produce detectable quantities of hydrogen or methane gas as fermentation products from a substrate consumed by the host under certain circumstances. Substrates include sugars such as lactulose, xylose, lactose, or glucose. The hydrogen (or methane) produced in the small intestine then enters the blood stream of the host and are gradually exhaled.

[0173] To perform the breath tests, the patient, after an overnight fast, swallows a controlled quantity of a suitable substrate, such as lactulose, xylose, lactose, or glucose, and breath samples are taken at frequent time intervals (e.g., every 10 to 15 minutes) for a two- to four-hour period. Samples are analyzed by gas chromatography or by other suitable techniques, singly or in combination. Plots of breath hydrogen in patients with SIBO typically show a double peak, i.e., a smaller early hydrogen peak followed by a larger hydrogen peak. A single hydrogen peak can also be an indicator of SIBO, if peak breath hydrogen exceeds the normal range of hydrogen for a particular testing protocol. (See, G. Mastropaolo and W. D. Rees, Gut 28(6):721-25 (1987)).

[0174] A variable fraction of the population fails to exhale appreciable hydrogen gas during intestinal fermentation of lactulose; the intestinal microflora of these individuals instead produce more methane. (G. Corazza et al., Dig. Dis. Sci. 38(11):2010-16 (1993); S. M. Riordan et al., Am. J. Gastroentrol. 91(9); 1795-1803 (1996)). Consequently, in the event of an initial negative result for breath hydrogen, or as a precaution, methane and / or carbon dioxide contents in each breath sample are optionally measured, in addition to hydrogen, or an alternative substrate is used.

[0175] In some embodiments, the presence of SIBO is demonstrated by a relative decrease in peak hydrogen exhalation values for an individual subject after antimicrobial treatment, in accordance with the present disclosure, compared to pretreatment values.

[0176] Another exemplary method of detecting bacterial overgrowth is by gas chromatography with mass spectrometry and / or radiation detection to measure breath emissions of isotope-labeled carbon dioxide, methane, or hydrogen, after administering an isotope-labeled substrate that is metabolizable by gastrointestinal bacteria but poorly digestible by the human host, such as lactulose, xylose, mannitol, or urea. (e.g., G. R. Swart and J. W. van den Berg, Scand. J. Gastroenterol. [Suppl.] 225:13-18 (1998); S. F. Dellert et al., J. Pediatr. Gastroenterol. Nutr. 25(2):153-58 (1997); C. E. King and P. P. Toskes, Crit. Rev. Lab. Sci. 21(3):269-81 (1984)). A poorly digestible substrate is one for which there is a relative or absolute lack of capacity in a human for absorption or for enzymatic degradation or catabolism thereof.

[0177] Suitable isotopic labels include 13< C or 14< C. For measuring methane or carbon dioxide, suitable isotopic labels can also include 2< H and 3< H or 17< O and 18< O, as long as the substrate is synthesized with the isotopic label placed in a metabolically suitable location in the structure of the substrate, e.g., a location where enzymatic biodegradation by intestinal microflora results in the isotopic label being sequestered in the gaseous product. If the isotopic label selected is a radioisotope, such as 14< C, 13< H, or 15< O, breath samples can be analyzed by gas chromatography with suitable radiation detection means. (e.g., C. S. Chang et al., Eur. J. Nucl. Med. 22(10):1118-22 (1995); C. E. King and P. P. Toskes, Gastroenterol. 91(6):1447-51 (1986); A. Schneider et al., 32(2):86-91 (1985)).

[0178] In some embodiments, SIBO is diagnosed by a presentation of symptomology suggestive of SIBO (e.g., bloating, diarrhea, flatulence, increased or reduced stool frequency, abdominal pain, constipation, weight loss, fever, abdominal tenderness, nausea, gastric stasis, steatorrhea, and any combination thereof). In some embodiments, SIBO is diagnosed by a presentation of symptomology suggestive of SIBO in combination with any of the other diagnostic methods described herein (e.g., a greater than about 1×10 3< CFU / mL in a small intestine fluid sample and / or the type of bacteria detected in the small intestine fluid sample).

[0179] As described herein, a patient diagnosed as having SIBO is administered one of ertapenem, meropenem, ceftriaxone, and piperacillin-tazobactam based on said diagnosis.Microbiome Characterization

[0180] Described herein are methods of characterizing the GI microbiome of a subject. As discussed above, the GI tract includes hundreds of microbial species, including bacteria, viruses, protozoan, and other parasites. The majority of gut bacteria belong to two phyla, the Bacteroidetes and Firmicutes; other phyla include Proteobacteria, Actinobacteria, Synergistetes and Fusobacteria. A healthy microbiota provides many benefits including resistance to colonization by harmful pathogens, metabolism of indigestible carbohydrates, vitamin production, and host immune response modulation (Browne et al. (2017) Nat. Rev. Microbiol. 15(9):531-43). Disruptions in the gut microbiota, also called dysbiosis, can lead to GI disorders, as well as metabolic disorders, and brain dysfunction (see Lin and Zhang (2017) BMC Immunol. 18:2). Thus, monitoring and characterizing the gut microbiota is an important tool in the armory of diagnostic / therapeutics tools relating to GIDs.

[0181] In some disclosuresof any of the methods described herein, an ingestible device described herein is administered to a subject to identify, characterize and / or analyze the GI microbiota. As described in detail below, the ingestible devices described herein may be used to collect a sample from the GI tract of the subject. Upon expulsion of the ingestible device from the subject, the device may be collected, and the sample therein may be further processed in order to characterize the microorganisms present at the site of collection. By collecting samples from different sites along the GI tract of a subject, the microbiota present at any location in the gastrointestinal tract can be mapped. For example, samples from one or more of the duodenum, jejunum, ileum, ascending colon, transverse colon or descending colon can be collected in order to analyze the microbiome of a subject. The location of particular species and strains of microorganisms present in the GI tract can be ascertained as described herein and a map of the general location of these microorganisms can be generated.

[0182] Any microorganisms can be identified and characterized using the methods described herein including, but not limited to bacteria, archaea, viruses, protozoa, parasites, and prions. In some disclosures, commensal bacteria are identified and characterized. In some disclosures, pathogenic bacteria are identified and characterized. Exemplary bacteria genera that may be identified and characterized include Acetanaerobacterium, Acetivibrio, Actinobacillus, Actinomyces, Aeromonas, Aggregatibacter, Alicyclobacillus, Alkaliphilus, Alstipes, Anaerophaga, Anaerofustis, Anaerosporobacter, Anaerostipes, Anaerotruncus, Anoxybacillus, Atopobium, Bacillus, Bacteroides, Blautia, Brachyspira, Brevibacillus, Bryantella, Bulleidia, Butyricicoccus, Butyrivibrio, Campylobacter, Capnocytophaga, Catenibacterium, Catonella, Chlamydiales, Citrobacter, Clostridiales, Clostridium, Collinsella, Corynebacterium, Coprobacillus, Coprococcus, Coxiella, Deferribacteres, Desulfitobacterium, Desulfotomaculum, Dialister, Dorea, Eggerthella, Escherichia, Enterobacter, Enterococcus, Erysipelothrix, Erysipelotrichaceae, Ethanoligenens, Eubacterium, Faecalibacterium, Filifactor, Flavonifractor, Flexistipes, Fulvimonas, Fusobacterium, Gemella, Gemmiger, Geobacillus, Gloeobacter, Granulicatella, Haemophilus, Helicobacter, Holdemania, Hydrogenoanaerobacterium, Kingella, Klebsiella, Kocuria, Lachnobacterium, Lachnoclostridium, Lachnospira, Lactobacillus, Lactonifactor, Leptospira, Leptotrichia, Lutispora, Lysinibacillus, Megasphaera, Mollicutes, Moorella, Moryella, Neisseria, Nocardia, Oribacterium, Oscillibacter, Oscillospira, Paenibacillus, Paludibacter, Papillibacter, Parabacteroides, Parascardovia, Peptostreptococcus, Plesiomonas, Porphyromonas, Prevotella, Proteus, Pseudoflavoniftactor, Pseudomonas, Ralstonia, Robinsoniella, Roseburia, Rothia, Ruminococcaceae, Ruminococcus, Saccharomonospora, Sarcina, Salmonella, Selenomonas, Sporobacter, Staphylococcus, Streptococcus, Solobacterium, Shigella, Sporobacter, Sporolactobacillus, Streptomyces, Subdoligranulum, Sutterella, Staphylococcus, Syntrophococcus, Tanerella, Thermoanaerobacter, Thermobifida, Treponema, Turicibacter, Vibrio, Veillonella, and Yersinia.

[0183] The ingestible devices described herein may directly characterize (without needing to process the sample ex vivo) microorganisms collected from the GI tract of a subject as provided in detail below. Moreover, the ingestible devices described herein may be used to collect a sample from the GI tract of a subject which can then be processed ex vivo in order to ascertain the identity, quantity, and characteristics of the microorganisms in the sample. In some disclosures, this analysis is performed using live cells (e.g., growing or non-growing cells) obtained from the sample. In some disclosures, this analysis is performed using dead cells obtained from the sample. For instance, samples collected from the device may be analyzed using methods known in the art for these purposes, including direct observation using dark-field microscopy (with and without staining), electron microscopy, microcolony detection by autofluorescence, fluorescence in situ hybridization (FISH), flow cytometry, differential system reactivity assays such as pH-based reactions, enzyme profiling, carbon source utilization, and the analysis of carbohydrate utilization, preformed enzymes, organic products, and cellular fatty acids, 16S ribosomal RNA sequencing, 23S ribosomal RNA sequencing, 18S ribosomal RNA sequencing, internal transcribed spacer (ITS) region sequencing, rpoB gene sequencing, serological testing, PCR, real time PCR, and matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) (see, e.g., Lagier et al. (2015) Clin. Microbiol. Rev. 28(1):237-64). In addition, assays that detect microbial byproducts (e.g., metabolites), toxins and antigens may be used to determine the identity of microorganisms collected from the GI tract of a subject (e.g., ELISA assays and flow cytometry assays).

[0184] For instance, samples obtained using an ingestible device described herein can be used to inoculate a liquid or solid culture media for further expansion and identification of the microorganisms present in the sample. For example, to identify bacteria, plates holding one of the following culture media can be inoculated with the sample either manually (e.g. using a sterile loop or needle) or by an automated streaker instrument: blood agar (BAP), Hektoen-enteric agar, Maconkey (MAC) agar, colistin-nalidix acid (CNA), candida ID agar, and MCA bifidobacter agar. The plates are then incubated (e.g., at 30-37 °C) for a number of hours (e.g., 8-96 hours or more) prior to evaluation. Some plates (e.g., the bifidobacter agar plates can be incubated longer (e.g., at 35 °C for at least or about 72 hours). Candida ID agar plates can be incubated for at least or about 72 hours at 35 °C. Following incubation, the plates can be assessed in various ways. For example, changes in morphology can be evaluated. CNA plates can be evaluated for alpha-hemolysis (green), gamma-hemolysis (no hemolysis) and / or beta-hemolysis (clearing of agar immediately surrounding a colony). Lactobacillus, Streptococcus, and Staphylococcus are a few of the isolates that may be recovered from CNA plates. HE agar plates can be examined for the presence of lactose (yellow) and non-lactose fermenters, hydrogen sulfide producers (black pigment) and clearly mucoid colonies. These plates are useful in isolating Salmonella, which produce hydrogen sulfide, and Shigella, which do not ferment lactose and appear as clear colonies. Maconkey agar can be used to identify gram-negative organisms. Almost all enteric bacilli will grow on this media. Lactose fermenting colonies (pink), non-lactose fermenting colonies (grayish or colorless), and mucoid colonies may also grow on these plates. Additional media and conditions for culturing human GI microbiota are described in Table 3 of Lagier et al. (2015) Clin. Microbiol. Rev. 28(1):237-64).

[0185] In some , samples obtained from the ingestible devices are subjected to further analysis in order to characterize the isolates species, strain, and antibiotic susceptibility. It will be readily understood by those of skill in the art that depending on the analysis methodology used, culture steps may be necessary in order to obtain individual microbial isolates for analysis. For example, MALDI-TOF analysis is a rapid, low cost method for identifying microorganisms. Three systems are available for the identification of microorganisms, the Andromas database (Andromas SAS, Paris, France), the Vitek-MS platform (bioMerieux, Marcy l'Etoile, France), and the Bruker Biotyper (Bruker Daltonics, Heidelberg, Germany; and Becton Dickinson, Franklin Lakes, NJ, USA) (see, e.g., Clark et al. (2013) Clin. Microbiol. Rev. 26:547-603. In some disclosures, samples obtained from the ingestible device or isolates obtained from the samples can be analyzed using a combination of polymerase chain reaction / electrospray ionization mass spectrometry (PCR / ESI-MS) to identify the microorganisms in the samples, such as the IRIDICA System (Abbot Molecular, Des Plaines, IL, USA). In some disclosures, samples obtained from the ingestible device or isolates obtained from the samples can be characterized using API ®< strips (bioMerieux, Marcy l'Etoile, France), which allow for the identification of bacteria (e.g., Staphylococci, Enterococci, Streptococci, Enterobacteriaceae, non-fermenting bacteria, and yeast) based on the detection of enzymatic activity.Sulfur-metabolizing bacteria

[0186] In some disclosures, the devices and methods described herein are used to identify, characterize and / or quantify sulfur-metabolizing microorganisms in the GI tract of a subject (e.g., in vivo or ex vivo), or the abundance of sulfated metabolites (e.g., bile acids, polyphenols and biogenic amines). For example, the microbiome of IBD patients with active disease may be enriched in microbial taxa involved in sulfur metabolism such as Escherichia, Shigella and Fusobacterium, and a high proportion of sulfate-reducing bacteria such as Desulfovibrio and Campylobacter.Mucin-degrading bacteria

[0187] In some disclosures, the devices and methods described herein are used to identify, characterize and / or quantify mucin-degrading microorganisms in the GI tract of a subject (e.g., in vivo or ex vivo), or the abundance of mucin or mucin metabolites. For example, the microbiome of ulcerative colitis and Crohn's disease patients may be enriched in R. torques and R. gnavus, while A. muciniphila, may be reduced in ulcerative colitis and Crohn's disease patients.Methane-producing archaea

[0188] In some disclosures, the devices and methods described herein may be used to identify, characterize and / or quantify methane-producing microorganism in the GI tract of a subject (e.g., in vivo or ex vivo). Archaea are the only confirmed, naturally-occurring biological sources of methane. Methanogenic archaea oxidize hydrogen to produce methane. Methanobrevibacter smithii is the predominant methanogen in the human intestine, although other methanogenic archaea may also be present, such as Methanosphaera stadtmanae and . Methanobacterium ruminatum. An association between IBS-C and high breath methane levels has been reported, and experimental evidence suggests that methane may delay intestinal transit and contractility (Triantafyllou et al. (2014) J. Neurogastroenterol. Motil. 20:31-40; and Goettlieb et al. (2016) Aliment. Pharmacol. Ther. 43(2):197-212. Further, a correlation between decreased methane production (assessed using methane on lactulose breath test) was observed in subjects who were responsive to antibiotic treatment for SIBO (Gatta and Scarpignato (2017) Aliment. Pharmacol. Ther. 45(5):604-16. Thus, methanogenic archaea may play an important role in many gastrointestinal diseases, including IBS and SIBO.

[0189] In some disclosures, the methods described herein include detecting the presence of and / or quantitating the amount of archaeal cells (e.g., methanogenic archaeal cells) present in a sample obtained from the GI tract of the subject. Assays for detecting the presence and / or quantity of bacteria in a sample obtained from the GI tract of a subject described herein may also be used to detect and / or quantify archaeal cells in a sample, including for example, the assays described below which detect (e.g., directly or indirectly) fluorescence emitted by coenzyme F-420.

[0190] In some disclosures, the methods described herein include determining the concentration of methane in the GI tract of a subj ect using an ingestible device described herein. For example, the concentration of methane can be detected at specific regions of the GI tract of a subject (e.g., one or more of the duodenum, jejunum, ileum, ascending colon, transverse colon or descending colon). In some disclosures, the methods described herein include identifying subject having an elevated level of methane in the GI tract as determined using a breath test, and further determining the concentration of methane in the GI tract of a subject using an ingestible device described herein. In some disclosures, the subject had or is at risk of developing a gastrointestinal disorder (e.g., SIBO and IBS).

[0191] In some disclosures, the methods described herein include methods for detecting volatile organic compounds (VOCs), such as methane, and other gases from a biological sample using resistive metal oxide gas sensors / mixed metal oxide gas sensors, electrochemical gas sensors, optical / IR gas sensors, conducting polymer / composite polymer resistive / capacitive gas sensors, quartz crystal microbalance gas sensors, carbon nanotubes, and pellister / calorimetric gas sensors in an ingestible device. Examples of ingestible gas sensors are described in US Patent Publication No. US 2013 / 0289368, which published on October 31, 2013, US Patent Publication No. US 2017 / 0284956, which published on October 5, 2017, and PCT Patent Publication No. WO 2016 / 197181, which published on December 15, 2016. Examples of gases that can be detected in the gastrointestinal tract using a sensor include, but are not limited to, oxygen, hydrogen, nitrogen, methane, and carbon dioxide.

[0192] In some disclosures, the methods described herein include generating spectral data of one or more regions of the GI tract of a subject using an ingestible device described herein. For example, the spectral data can be generated for specific regions of the GI tract of a subject (e.g., one or more of the duodenum, jejunum, ileum, ascending colon, transverse colon or descending colon).

[0193] In some disclosures, one or more of the following conditions may be determined for one or more regions of the GI tract of a subject using an ingestible device described herein: pH, gastrointestinal motility, temperature, heart rate, and respiration rate.

[0194] In some disclosures, the methods and devices described herein are used to generate a microbial profile of a subject. The microbial profile can include information such as the identity, location, abundance, antibiotic-resistance, antibiotic-sensitivity of microorganisms (e.g., commensal or pathogenic bacteria) present in the GI tract of a subject. A microbial profile can include information relating to any analyte described herein, pH, temperature, gastrointestinal motility, and others.

[0195] In some disclosures, a microbial profile can be generated for a subject having a GID (e.g., FBS or SIBO). In some embodiments, a microbial profile can be generated for a subject before and after treatment with a therapeutic agent (e.g., an antibiotic). The microbial profile of a subject may be used to predict a subject's response to a treatment (e.g., an antibiotic treatment for an infection; see, e.g., Khanna et al. (2016) Aliment. Pharmacol. Ther. 44(7):715-27).

[0196] In some disclosures, a microbial profile can be generated for a subject before and after consumption of an ingestible standard. Ingestible standards allow for the comparison of microbial profiles from the same individual at different time points as well as from different individuals (e.g., having different genetic profiles). Ingestible standards can be used to ascertain how particular foods or macronutrients affect the microbial composition of the microbiome of a subject. In some disclosures, a microbial profile can be generated for a healthy subject. In some disclosures, a microbial profile can be generated for a malnourished subject.

[0197] In some disclosures, a microbial profile can be generated for a subject before and after consumption of an medical food to develop a "nutrient profile" for the subject. The term "medical food" refers to a food which is formulated to be consumed or administered under the supervision of a physician and which is intended for the specific dietary management of a disease or condition for which distinctive nutritional requirements are established. In some disclosures, an ingestible device described herein may be administered to a subject before and / or after ingestion of a medical food, and a sample obtained from the GI tract of the subject using the ingestible device may be analyzed to determine levels of one or more micronutrients, macronutrients, enzymes, amino acids, fats, carbohydrates, vitamins (e.g., folic acid, vitamin B6, vitamin B12, biotin, thiamine, riboflavin, niacin, vitamin B5, vitamin A, vitamin C, vitamin D, and vitamin E), minerals (e.g., calcium, chromium, chloride, copper, iodide, fluoride, magnesium, manganese, molybdenum, potassium, phosphorous, selenium, sodium, and zinc) present in the GI tract of the subject. In some disclosures, an ingestible device described herein may be administered to a subject before and / or after ingestion of a medical food, and a sample obtained from the GI tract of the subject using the ingestible device may be analyzed to characterize the microbiome present in the GI tract of the subject before and / or after ingesting the medical food.Antimicrobial Susceptibility Testing

[0198] In some disclosures, individual bacterial isolates obtained from the cultures above are subjected to antimicrobial susceptibility testing to determine their resistance and / or susceptibility to specific antimicrobial agents. This information may be used to determine an appropriate antibiotic treatment to, for example, treat a GI infection with a specific pathogen, decrease / increase the amount of a particular bacterial strain / species in the GI tract of the subject, and / or treat SIBO in a subject. Thus, once an antimicrobial profile has been obtained for a bacterial isolate of interest, an appropriate antimicrobial can be administered to the subject as desired.

[0199] Susceptibility testing is particular useful to detect individual isolates that possess acquired antimicrobial resistance mechanisms. Many susceptibility testing methods are known in the art and can be used as described herein (see, e.g., Jorgensen and Ferraro (2009) Clinical Infectious Diseases 49:1749-1755; and Maurer et al. (2017) Infectious Disease Reports 9:6839). For example, antimicrobial susceptibility can be determined using conventional culture based methods such as the broth or agar dilution test. In these dilution tests, the bacterial isolate of interest is inoculated onto different media that include serial dilutions of an antimicrobial agent, and incubated under appropriate conditions (e.g., overnight at 37 °C) to allow for growth to occur. Following the incubation period, the media is examined to determine bacterial growth. The lowest concentration of antibiotic that prevents growth represents the minimal inhibitory concentration (MIC). Broth dilution tests can be miniaturized and mechanized allowing for reproducibility and high throughput.

[0200] The antimicrobial gradient method can also be used. The antimicrobial gradient method relies on the creation of an antimicrobial concentration gradient in an agar medium to determine susceptibility. The Etest ®< (bioMerieux, Marcy l'Etoile, France) is a commercial version of the test that employs thin plastic strips impregnated on the underside with a dried antimicrobial concentration gradient, and include a marking of the concentration scale of the antimicrobial. The strips are placed in a radial fashion on a agar plate that has been inoculated with a bacterial isolate of interest. After incubation under appropriate conditions (e.g., overnight at 37 °C) to allow for growth to occur. If the antibiotic inhibits growth of the bacterial isolate, a growth inhibition area forms in the shape of an ellipse where no bacterial growth is detected. The MIC is determined as the concentration indicated on the strip corresponding to the lower part of the ellipse-shaped growth inhibition area.

[0201] Another type of susceptibility test is the disk diffusion test, often referred to as the Kirby-Bauer test. This is a standardized test that involves inoculating a gel plate (e.g., a 150-mm Mueller-Hinton agar plate) and placing thereon one or more disks impregnated with fixed concentrations of an antimicrobial. After incubation (e.g., 18-24 hours at 35 °C.), the diameter of zones of inhibition around the disks (if present) determine the sensitivity of the inoculated microorganism to the particular antimicrobial agent impregnated in each disk. Results of this method can be analyzed by comparing the diameter of the inhibition zone with information published by the National Committee on Clinical Laboratory Standards.

[0202] Commercial instruments for antimicrobial susceptibility testing, such as Phoenix 100 (BD Biosciences) and Vitek ®< 2 (BioMérieux), allow automation and reduce hands-on and incubation time, and can be used in the methods described herein. Both instruments operate with colorimetric or fluorimetric indicators for bacterial identification and estimation of growth rate.

[0203] In some disclosures, individual microbial isolates (e.g., bacteria, archaea, protozoa, and parasites) obtained from a sample collected from the GI tract of a subject (e.g., a subject having a GID or GID symptomology) are analyzed to determine their resistance and / or susceptibility to particular antimicrobial agents (e.g., an antibiotic described herein). This analysis can be used to determine effective antimicrobial treatment regimens to treat against the microbial isolate. For example, if the microbial isolate is a pathogen, suitable antimicrobial treatments for the subject can be identified.

[0204] In some disclosures, the susceptibility and / or resistance of a microorganism in the GI tract of a subject to an antimicrobial agent can be determined by collecting a sample from the GI tract using an ingestible device described herein. The ingestible device may include one or more sampling chambers, comprising one or more antimicrobial agents. Samples may be recovered from the device after a period of time (e.g., about 1 hour, about 3 hours, about 6 hours, about 12 hours, about 18 hours, about 24 hours, about 36 hours, about 48 hours, about 72 hours or more) and analyzed to quantitate and / or determine the viability of the microorganism(s) in the sample. Reduced viability (e.g., determined by analyzing the dead microorganisms recovered from the sample) indicates that a microorganism is susceptible to the antimicrobial agent(s) that was in the sampling chamber. Viability indicates that the microorganism is resistant to the antimicrobial agent(s) that was in the sampling chamber. Microorganism viability can be determined by a variety of methods, and can include both methods that highlight viable organisms (vital stains) as well as dead organisms (mortal stains). Stains for assessing viability are known in the art and include ethidium or propidium dyes, hexidium iodide, SYTO nucleic acid stains, 7-aminiactinomycin D, SYTOX Green / Orange / Blue nucleic acid stains, and others (see, e.g., Lloyd and Hayes (1995) FEMS Microbiology Letters 133:1-7). Viable and dead microorganisms recovered from the sample can be identified using a method described herein.

[0205] Any antimicrobial may be tested using the methods described herein, including beta-lactam antibiotics, aminoglycosides, ansa-type antibiotics, anthraquinones, antibiotic azoles, antibiotic glycopeptides, macrolides, antibiotic nucleosides, antibiotic peptides, antibiotic polyenes, antibiotic polyethers, quinolones, antibiotic steroids, sulfonamides, carbapenems, tetracycline, dicarboxylic acids, antibiotic metals, oxidizing agents, substances that release free radicals and / or active oxygen, cationic antimicrobial agents, quaternary ammonium compounds, biguanides, triguanides, bisbiguanides and analogs and polymers thereof and naturally occurring antibiotic compounds.

[0206] Beta-lactam antibiotics include, but are not limited to, 2-(3-alanyl)clavam, 2-hydroxymethylclavam, 8-epi-thienamycin, acetyl-thienamycin, amoxicillin, amoxicillin sodium, amoxicillin trihydrate, amoxicillin-potassium clavulanate combination, ampicillin, ampicillin sodium, ampicillin trihydrate, ampicillin-sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, bacampicillin, biapenem, carbenicillin, carbenicillin disodium, carfecillin, carindacillin, carpetimycin, cefacetril, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefamandole, cefapirin, cefatrizine, cefatrizine propylene glycol, cefazedone, cefazolin, cefbuperazone, cefcapene, cefcapene pivoxil hydrochloride, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefetamet, cefetamet pivoxil, cefixime, cefinenoxime, cefinetazole, cefminox, cefminox, cefmolexin, cefodizime, cefonicid, cefoperazone, ceforanide, cefoselis, cefotaxime, cefotetan, cefotiam, cefoxitin, cefozopran, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefprozil, cefquinome, cefradine, cefroxadine, cefsulodin, ceftazidime, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftizoxime, ceftriaxone, cefuroxime, cefuroxime axetil, cephalosporin, cephamycin, chitinovorin, ciclacillin, clavulanic acid, clometocillin, cloxacillin, cycloserine, deoxy pluracidomycin, dicloxacillin, dihydro pluracidomycin, epicillin, epithienamycin, ertapenem, faropenem, flomoxef, flucloxacillin, hetacillin, imipenem, lenampicillin, loracarbef, mecillinam, meropenem, metampicillin, meticillin, mezlocillin, moxalactam, nafcillin, northienamycin, oxacillin, panipenem, penamecillin, penicillin, phenethicillin, piperacillin, tazobactam, pivampicillin, pivcefalexin, pivmecillinam, pivmecillinam hydrochloride, pluracidomycin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, talampicillin, temocillin, terconazole, thienamycin, ticarcillin and analogs, salts and derivatives thereof.

[0207] Beta-lactam antibiotics can be used in combination with other antibiotics or active agents to achieve an antimicrobial effect. For example, Beta-lactam antibiotics (such as carbapenems) can be co-administered with carbapenemase inhibitors (e.g., sulbactam, tazobactam, clavulanic acid, avibactam, vaborbactam). Use of such inhibitors restores or increases potency to carbapenem antibiotics by inhibiting the beta-lactamase enzymes that would otherwise degrade them. Other exemplary inhibitors are relebactam and boronic acid-based inhibitors, including PRX7009, b-lactamase inhibitory protein II, and Zinc01807204 and Zinc02318494 compounds. Metallo-b-lactamase inhibitors include EDTA, thioester derivatives, propionic acid, maleic acid, succinic acid and phthalic acid derivatives.

[0208] Aminoglycosides include, but are not limited to, 1,2'-N-DL-isoseryl-3',4'-dideoxykanamycin B, 1,2'-N-DL-isoseryl-kanamycin B, 1,2'-N-[(S)-4-amino-2-hydroxybutyryl]-3',4'-dideoxykanamycin B, 1,2'-N-[(S)-4-amino-2-hydroxybutyryl]-kanamycin B, 1-N-(2-Aminobutanesulfonyl) kanamycin A, 1-N-(2-aminoethanesulfonyl)3',4'-dideoxyribostamycin, 1-N-(2-Aminoethanesulfonyl)3'-deoxyribostamycin, 1-N-(2-aminoethanesulfonyl)3'4'-dideoxykanamycin B, 1-N-(2-aminoethanesulfonyl)kanamycin A, 1-N-(2-aminoethanesulfonyl)kanamycin B, 1-N-(2-aminoethanesulfonyl)ribostamycin, 1-N-(2-aminopropanesulfonyl)3'-deoxykanamycin B, 1-N-(2-aminopropanesulfonyl)3'4'-dideoxykanamycin B, 1-N-(2-aminopropanesulfonyl)kanamycin A, 1-N-(2-aminopropanesulfonyl)kanamycin B, 1-N-(L-4-amino-2-hydroxy-butyryl)2,'3'-dideoxy-2'-fluorokanamycin A, 1-N-(L-4-amino-2-hydroxy-propionyl)2,'3'-dideoxy-2'-fluorokanamycin A, 1-N-DL-3',4'-dideoxy-isoserylkanamycin B, 1-N-DL-isoserylkanamycin, 1-N-DL-isoserylkanamycin B, 1-N-[L-(-)-(alpha-hydroxy-gamma-aminobutyryl)]-XK-62-2,2',3'-dideoxy-2'-fluorokanamycin A,2-hydroxygentamycin A3,2-hydroxygentamycin B, 2-hydroxygentamycin B1, 2-hydroxygentamycin JI-20A, 2-hydroxygentamycin JI-20B, 3"-N-methyl-4"-C-methyl-3',4'-dodeoxy kanamycin A, 3"-N-methyl-4"-C-methyl-3',4'-dodeoxy kanamycin B, 3"-N-methyl-4"-C-methyl-3',4'-dodeoxy-6'-methyl kanamycin B, 3',4'-Dideoxy-3'-eno-ribostamycin,3',4'-dideoxyneamine,3',4'-dideoxyribostamycin, 3'-deoxy-6'-N-methyl-kanamycin B,3'-deoxyneamine,3'-deoxyribostamycin, 3'-oxysaccharocin,3,3'-nepotrehalosadiamine, 3-demethoxy-2"-N-formimidoylistamycin B disulfate tetrahydrate, 3-demethoxyistamycin B,3-O-demethyl-2-N-formimidoylistamycin B, 3-O-demethylistamycin B,3-trehalosamine,4",6"-dideoxydibekacin, 4-N-glycyl-KA-6606VI, 5"-Amino-3',4',5"-trideoxy-butirosin A, 6"-deoxydibekacin,6'-epifortimicin A, 6-deoxy-neomycin (structure 6-deoxy-neomycin B),6-deoxy-neomycin B, 6-deoxy-neomycin C, 6-deoxy-paromomycin, acmimycin, AHB-3',4'-dideoxyribostamycin, AHB-3'-deoxykanamycin B, AHB-3'-deoxyneamine, AHB-3'-deoxyribostamycin, AHB-4"-6"-dideoxydibekacin, AHB-6"-deoxydibekacin, AHB-dideoxyneamine, AHB-kanamycin B, AHB-methyl-3'-deoxykanamycin B, amikacin, amikacin sulfate, apramycin, arbekacin, astromicin, astromicin sulfate, bekanamycin, bluensomycin, boholmycin, butirosin, butirosin B, catenulin, coumamidine gamma1, coumamidine gamma2,D,L-1-N-(alpha-hydroxy-beta-aminopropionyl)-XK-62-2, dactimicin, de-O-methyl-4-N-glycyl-KA-6606VI, de-O-methyl-KA-6606I, de-O-methyl-KA-7038I, destomycin A, destomycin B, di-N6',O3-demethylistamycin A, dibekacin, dibekacin sulfate, dihydrostreptomycin, dihydrostreptomycin sulfate, epi-formamidoylglycidylfortimicin B, epihygromycin, formimidoyl-istamycin A, formimidoyl-istamycin B, fortimicin B, fortimicin C, fortimicin D, fortimicin KE, fortimicin KF, fortimicin KG, fortimicin KG1 (stereoisomer KG1 / KG2), fortimicin KG2 (stereoisomer KG1 / KG2), fortimicin KG3, framycetin, framycetin sulphate, gentamicin, gentamycin sulfate, globeomycin, hybrimycin A1, hybrimycin A2, hybrimycin B1, hybrimycin B2, hybrimycin C1, hybrimycin C2, hydroxystreptomycin, hygromycin, hygromycin B, isepamicin, isepamicin sulfate, istamycin, kanamycin, kanamycin sulphate, kasugamycin, lividomycin, marcomycin, micronomicin, micronomicin sulfate, mutamicin, myomycin, N-demethyl-7-O-demethylcelesticetin, demethylcelesticetin, methanesulfonic acid derivative of istamycin, nebramycin, nebramycin, neomycin, netilmicin, oligostatin, paromomycin, quintomycin, ribostamycin, saccharocin, seldomycin, sisomicin, sorbistin, spectinomycin, streptomycin, tobramycin, trehalosmaine, trestatin, validamycin, verdamycin, xylostasin, zygomycin and analogs, salts and derivatives thereof.

[0209] Ansa-type antibiotics include, but are not limited to, 21-hydroxy-25-demethyl-25-methyl-thioprotostreptovaricin, 3-methyl-thiorifamycin, ansamitocin, atropisostreptovaricin, awamycin, halomicin, maytansine, naphthomycin, rifabutin, rifamide, rifampicin, rifamycin, rifapentine, rifaximin (e.g., Xifaxan ®< ), rubradirin, streptovaricin, tolypomycin and analogs, salts and derivatives thereof.

[0210] Antibiotic anthraquinones include, but are not limited to, auramycin, cinerubin, ditrisarubicin, ditrisarubicin C, figaroic acid fragilomycin, minomycin, rabelomycin, rudolfomycin, sulfurmycin and analogs, salts and derivatives thereof.

[0211] Antibiotic azoles include, but are not limited to, azanidazole, bifonazole, butoconazol, chlormidazole, chlormidazole hydrochloride, cloconazole, cloconazole monohydrochloride, clotrimazol, dimetridazole, econazole, econazole nitrate, enilconazole, fenticonazole, fenticonazole nitrate, fezatione, fluconazole, flutrimazole, isoconazole, isoconazole nitrate, itraconazole, ketoconazole, lanoconazole, metronidazole, metronidazole benzoate, miconazole, miconazole nitrate, neticonazole, nimorazole, niridazole, omoconazol, ornidazole, oxiconazole, oxiconazole nitrate, propenidazole, secnidazol, sertaconazole, sertaconazole nitrate, sulconazole, sulconazole nitrate, tinidazole, tioconazole, voriconazol and analogs, salts and derivatives thereof.

[0212] Antibiotic glycopeptides include, but are not limited to, acanthomycin, actaplanin, avoparcin, balhimycin, bleomycin B (copper bleomycin), chloroorienticin, chloropolysporin, demethylvancomycin, enduracidin, galacardin, guanidylfungin, hachimycin, demethylvancomycin, N-nonanoyl-teicoplanin, phleomycin, platomycin, ristocetin, staphylocidin, talisomycin, teicoplanin, vancomycin, victomycin, xylocandin, zorbamycin and analogs, salts and derivatives thereof.

[0213] Macrolides include, but are not limited to, acetylleucomycin, acetylkitasamycin, angolamycin, azithromycin, bafilomycin, brefeldin, carbomycin, chalcomycin, cirramycin, clarithromycin, concanamycin, deisovaleryl-niddamycin, demycinosyl-mycinamycin, Di-O-methyltiacumicidin, dirithromycin, erythromycin, erythromycin estolate, erythromycin ethyl succinate, erythromycin lactobionate, erythromycin stearate, flurithromycin, focusin, foromacidin, haterumalide, haterumalide, josamycin, josamycin ropionate, juvenimycin, juvenimycin, kitasamycin, ketotiacumicin, lankavacidin, lankavamycin, leucomycin, machecin, maridomycin, megalomicin, methylleucomycin, methymycin, midecamycin, miocamycin, mycaminosyltylactone, mycinomycin, neutramycin, niddamycin, nonactin, oleandomycin, phenylacetyideltamycin, pamamycin, picromycin, rokitamycin, rosaramicin, roxithromycin, sedecamycin, shincomycin, spiramycin, swalpamycin, tacrolimus, telithromycin, tiacumicin, tilmicosin, treponemycin, troleandomycin, tylosin, venturicidin and analogs, salts and derivatives thereof.

[0214] Antibiotic nucleosides include, but are not limited to, amicetin, angustmycin, azathymidine, blasticidin S, epiroprim, flucytosine, gougerotin, mildiomycin, nikkomycin, nucleocidin, oxanosine, oxanosine, puromycin, pyrazomycin, showdomycin, sinefungin, sparsogenin, spicamycin, tunicamycin, uracil polyoxin, vengicide and analogs, salts and derivatives thereof.

[0215] Antibiotic peptides include, but are not limited to, actinomycin, aculeacin, alazopeptin, amfomycin, amythiamycin, antifungal from Zalerion arboricola, antrimycin, apid, apidaecin, aspartocin, auromomycin, bacileucin, bacillomycin, bacillopeptin, bacitracin, bagacidin, beminamycin, beta-alanyl-L-tyrosine, bottromycin, capreomycin, caspofungine, cepacidine, cerexin, cilofungin, circulin, colistin, cyclodepsipeptide, cytophagin, dactinomycin, daptomycin, decapeptide, desoxymulundocandin, echanomycin, echinocandin B, echinomycin, ecomycin, enniatin, etamycin, fabatin, ferrimycin, ferrimycin, ficellomycin, fluoronocathiacin, fusaricidin, gardimycin, gatavalin, globopeptin, glyphomycin, gramicidin, herbicolin, iomycin, iturin, iyomycin, izupeptin, janiemycin, janthinocin, jolipeptin, katanosin, killertoxin, lipopeptide antibiotic, lipopeptide from Zalerion sp., lysobactin, lysozyme, macromomycin, magainin, melittin, mersacidin, mikamycin, mureidomycin, mycoplanecin, mycosubtilin, neopeptifluorin, neoviridogrisein, netropsin, nisin, nocathiacin, nocathiacin 6-deoxyglycoside, nosiheptide, octapeptin, pacidamycin, pentadecapeptide, peptifluorin, permetin, phytoactin, phytostreptin, planothiocin, plusbacin, polcillin, polymyxin antibiotic complex, polymyxin B, polymyxin B1, polymyxin F, preneocarzinostatin, quinomycin, quinupristin-dalfopristin, safracin, salmycin, salmycin, salmycin, sandramycin, saramycetin, siomycin, sperabillin, sporamycin, a Streptomyces compound, subtilin, teicoplanin aglycone, telomycin, thermothiocin, thiopeptin, thiostrepton, tridecaptin, tsushimycin, tuberactinomycin, tuberactinomycin, tyrothricin, valinomycin, viomycin, virginiamycin, zervacin and analogs, salts and derivatives thereof.

[0216] In some disclosures, the antibiotic peptide is a naturally-occurring peptide that possesses an antibacterial and / or an antifungal activity. Such peptide can be obtained from an herbal or a vertebrate source.

[0217] Polyenes include, but are not limited to, amphotericin, amphotericin, aureofungin, ayfactin, azalomycin, blasticidin, candicidin, candicidin methyl ester, candimycin, candimycin methyl ester, chinopricin, filipin, flavofungin, fradicin, hamycin, hydropricin, levorin, lucensomycin, lucknomycin, mediocidin, mediocidin methyl ester, mepartricin, methyl amphotericin, natamycin, niphimycin, nystatin, nystatin methyl ester, oxypricin, partricin, pentamycin, perimycin, pimaricin, primycin, proticin, rimocidin, sistomycosin, sorangicin, trichomycin and analogs, salts and derivatives thereof.

[0218] Polyethers include, but are not limited to, 20-deoxy-epi-narasin, 20-deoxysalinomycin, carriomycin, dianemycin, dihydrolonomycin, etheromycin, ionomycin, iso-lasalocid, lasalocid, lenoremycin, lonomycin, lysocellin, monensin, narasin, oxolonomycin, a polycyclic ether antibiotic, salinomycin and analogs, salts and derivatives thereof.

[0219] Quinolones include, but are not limited to, an alkyl-methylendioxy-4(1H)-oxocinnoline-3-carboxylic acid, alatrofloxacin, cinoxacin, ciprofloxacin, ciprofloxacin hydrochloride, danofloxacin, dermofongin A, enoxacin, enrofloxacin, fleroxacin, flumequine, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, lomefloxacin, lomefloxacin, hydrochloride, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacine, pefloxacin, pefloxacin mesylate, pipemidic acid, piromidic acid, premafloxacin, rosoxacin, rufloxacin, sparfloxacin, temafloxacin, tosufloxacin, trovafloxacin and analogs, salts and derivatives thereof.

[0220] Antibiotic steroids include, but are not limited to, aminosterol, ascosteroside, cladosporide A, dihydrofusidic acid, dehydro-dihydrofusidic acid, dehydrofusidic acid, fusidic acid, squalamine and analogs, salts and derivatives thereof.

[0221] Sulfonamides include, but are not limited to, chloramine, dapsone, mafenide, phthalylsulfathiazole, succinylsulfathiazole, sulfabenzamide, sulfacetamide, sulfachlorpyridazine, sulfadiazine, sulfadiazine silver, sulfadicramide, sulfadimethoxine, sulfadoxine, sulfaguanidine, sulfalene, sulfamazone, sulfamerazine, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfamonomethoxine, sulfamoxol, sulfanilamide, sulfaperine, sulfaphenazol, sulfapyridine, sulfaquinoxaline, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfatolamide, sulfatriazin, sulfisomidine, sulfisoxazole, sulfisoxazole acetyl, sulfacarbamide and analogs, salts and derivatives thereof.

[0222] Tetracyclines include, but are not limited to, dihydrosteffimycin, demethyltetracycline, aclacinomycin, akrobomycin, baumycin, bromotetracycline, cetocyclin, chlortetracycline, clomocycline, daunorubicin, demeclocycline, doxorubicin, doxorubicin hydrochloride, doxycycline, lymecyclin, marcellomycin, meclocycline, meclocycline sulfosalicylate, methacycline, minocycline, minocycline hydrochloride, musettamycin, oxytetracycline, rhodirubin, rolitetracycline, rubomycin, serirubicin, steffimycin, tetracycline and analogs, salts and derivatives thereof.

[0223] Dicarboxylic acids, having between about 6 and about 14 carbon atoms in their carbon atom skeleton are particularly useful in the treatment of disorders of the skin and mucosal membranes that involve microbial. Suitable dicarboxylic acid moieties include, but are not limited to, adipic acid, pimelic acid, suberic acid, azelaic acid, sebacic acid, 1,11-undecanedioic acid, 1,12-dodecanedioic acid, 1,13-tridecanedioic acid and 1, 14-tetradecanedioic acid. Thus, in one or more disclosures of the present disclosure, dicarboxylic acids, having between about 6 and about 14 carbon atoms in their carbon atom skeleton, as well as their salts and derivatives (e.g., esters, amides, mercapto-derivatives, anhydraides), are useful immunomodulators in the treatment of disorders of the skin and mucosal membranes that involve inflammation. Azelaic acid and its salts and derivatives are preferred. It has antibacterial effects on both aerobic and anaerobic organisms, particularly Propionibacterium acnes and Staphylococcus epidermidis, normalizes keratinization, and has a cytotoxic effect on malignant or hyperactive melanocytes. In a preferred disclosure, the dicarboxylic acid is azelaic acid in a concentration greater than 10%. Preferably, the concentration of azelaic acid is between about 10% and about 25%. In such concentrates, azelaic acid is suitable for the treatment of a variety of skin disorders, such as acne, rosacea and hyperpigmentation.

[0224] In some disclosures, the antibiotic agent is an antibiotic metal. A number of metals ions have been shown to possess antibiotic activity, including silver, copper, zinc, mercury, tin, lead, bismutin, cadmium, chromium and ions thereof. It has been theorized that these antibiotic metal ions exert their effects by disrupting respiration and electron transport systems upon absorption into bacterial or fungal cells. Anti-microbial metal ions of silver, copper, zinc, and gold, in particular, are considered safe for in vivo use. Anti-microbial silver and silver ions are particularly useful due to the fact that they are not substantially absorbed into the body. Thus, in one or more disclosure, the antibiotic metal consists of an elemental metal, selected from the group consisting of silver, copper, zinc, mercury, tin, lead, bismutin, cadmium, chromium and gold, which is suspended in the composition as particles, microparticles, nanoparticles or colloidal particles. The antibiotic metal can further be intercalated in a chelating substrate.

[0225] In further disclosures, the antibiotic metal is ionic. The ionic antibiotic metal can be presented as an inorganic or organic salt (coupled with a counterion), an organometallic complex or an intercalate. Non-binding examples of counter inorganic and organic ions are sulfadiazine, acetate, benzoate, carbonate, iodate, iodide, lactate, laurate, nitrate, oxide, and palmitate, a negatively charged protein. In preferred embodiments, the antibiotic metal salt is a silver salt, such as silver acetate, silver benzoate, silver carbonate, silver iodate, silver iodide, silver lactate, silver laurate, silver nitrate, silver oxide, silver palmitate, silver protein, and silver sulfadiazine.

[0226] In one or more disclosures, the antibiotic metal or metal ion is embedded into a substrate, such as a polymer, or a mineral (such as zeolite, clay and silica).

[0227] In one or more disclosures, the antibiotic agent includes strong oxidants and free radical liberating compounds, such as oxygen, hydrogen peroxide, benzoyl peroxide, elemental halogen species, as well as oxygenated halogen species, bleaching agents (e.g., sodium, calcium or magnesium hypochloride and the like), perchlorite species, iodine, iodate, and benzoyl peroxide. Organic oxidizing agents, such as quinones, are also included. Such agents possess a potent broad-spectrum activity.

[0228] In one or more disclosures, the antibiotic agent is a cationic antimicrobial agent. The outermost surface of bacterial cells universally carries a net negative charge, making them sensitive to cationic substances. Examples of cationic antibiotic agents include: quaternary ammonium compounds (QAC's)-QAC's are surfactants, generally containing one quaternary nitrogen associated with at least one major hydrophobic moiety; alkyltrimethyl ammonium bromides are mixtures of where the alkyl group is between 8 and 18 carbons long, such as cetrimide (tetradecyltrimethylammonium bromide); benzalkonium chloride, which is a mixture of n-alkyldimethylbenzyl ammonium chloride where the alkyl groups (the hydrophobic moiety) can be of variable length; dialkylmethyl ammonium halides; dialkylbenzyl ammonium halides; and QAC dimmers, which bear bi-polar positive charges in conjunction with interstitial hydrophobic regions.

[0229] In one or more disclosures, the cationic antimicrobial agent is a polymer. Cationic antimicrobial polymers include, for example, guanide polymers, biguanide polymers, or polymers having side chains containing biguanide moieties or other cationic functional groups, such as benzalkonium groups or quarternium groups (e.g., quaternary amine groups). It is understood that the term "polymer" as used herein includes any organic material including three or more repeating units, and includes oligomers, polymers, copolymers, block copolymers, terpolymers, etc. The polymer backbone may be, for example a polyethylene, polypropylene or polysilane polymer.

[0230] In one or more disclosures, the cationic antimicrobial polymer is a polymeric biguanide compound. When applied to a substrate, such a polymer is known to form a barrier film that can engage and disrupt a microorganism. An exemplary polymeric biguanide compound is polyhexamethylene biguanide (PHMB) salts. Other exemplary biguanide polymers include, but are not limited to poly(hexamethylenebiguanide), poly(hexamethylenebiguanide) hydrochloride, poly(hexamethylenebiguanide) gluconate, poly(hexamethylenebiguanide) stearate, or a derivative thereof. In one or disclosures embodiments, the antimicrobial material is substantially water-insoluble.

[0231] In some disclosures, the antibiotic agent is selected from the group of biguanides, triguanides, bisbiguanides and analogs thereof.

[0232] Guanides, biguanides, biguanidines and triguanides are unsaturated nitrogen containing molecules that readily obtain one or more positive charges, which make them effective antimicrobial agents. The basic structures a guanide, a biguanide, a biguanidine and a triguanide are provided below. In some disclosures, the guanide, biguanide, biguanidine or triguanide, provide bi-polar configurations of cationic and hydrophobic domains within a single molecule.

[0233] Examples of guanides, biguanides, biguanidines and triguanides that are currently been used as antibacterial agents include chlorhexidine and chlorohexidine salts, analogs and derivatives, such as chlorhexidine acetate, chlorhexidine gluconate and chlorhexidine hydrochloride, picloxydine, alexidine and polihexanide. Other examples of guanides, biguanides, biguanidines and triguanides that can conceivably be used according to the present disclosure are chlorproguanil hydrochloride, proguanil hydrochloride (currently used as antimalarial agents), mefformin hydrochloride, phenformin and buformin hydrochloride (currently used as antidiabetic agents).

[0234] Yet, in one or more disclosures, the antibiotic is a non-classified antibiotic agent, including, without limitation, aabomycin, acetomycin, acetoxycycloheximide, acetylnanaomycin, an Actinoplanes sp. compound, actinopyrone, aflastatin, albacarcin, albacarcin, albofungin, albofungin, alisamycin, alpha-R,S-methoxycarbonylbenzylmonate, altromycin, amicetin, amycin, amycin demanoyl compound, amycine, amycomycin, anandimycin, anisomycin, anthramycin, anti-syphilis immune substance, anti-tuberculosis immune substance, an antibiotic from Escherichia coli, an antibiotic from Streptomyces refuineus, anticapsin, antimycin, aplasmomycin, aranorosin, aranorosinol, arugomycin, ascofuranone, ascomycin, ascosin, Aspergillus flavus antibiotic, asukamycin, aurantinin, an Aureolic acid antibiotic substance, aurodox, avilamycin, azidamfenicol, azidimycin, bacillaene, a Bacillus larvae antibiotic, bactobolin, benanomycin, benzanthrin, benzylmonate, bicozamycin, bravomicin, brodimoprim, butalactin, calcimycin, calvatic acid, candiplanecin, carumonam, carzinophilin, celesticetin, cepacin, cerulenin, cervinomycin, chartreusin, chloramphenicol, chloramphenicol palmitate, chloramphenicol succinate sodium, chlorflavonin, chlorobiocin, chlorocarcin, chromomycin, ciclopirox, ciclopirox olamine, citreamicin, cladosporin, clazamycin, clecarmycin, clindamycin, coliformin, collinomycin, copiamycin, corallopyronin, corynecandin, coumermycin, culpin, cuprimyxin, cyclamidomycin, cycloheximide, dactylomycin, danomycin, danubomycin, delaminomycin, demethoxyrapamycin, demethylscytophycin, dermadin, desdamethine, dexylosyl-benanomycin, pseudoaglycone, dihydromocimycin, dihydronancimycin, diumycin, dnacin, dorrigocin, dynemycin, dynemycin triacetate, ecteinascidin, efrotomycin, endomycin, ensanchomycin, equisetin, ericamycin, esperamicin, ethylmonate, everninomicin, feldamycin, flambamycin, flavensomycin, florfenicol, fluvomycin, fosfomycin, fosfonochlorin, fredericamycin, frenolicin, fumagillin, fumifungin, funginon, fusacandin, fusafungin, gelbecidine, glidobactin, grahamimycin, granaticin, griseofulvin, griseoviridin, grisonomycin, hayumicin, hayumicin, hazymicin, hedamycin, heneicomycin, heptelicid acid, holomycin, humidin, isohematinic acid, karnatakin, kazusamycin, kristenin, L-dihydrophenylalanine, a L-isoleucyl-L-2-amino-4-(4'-amino-2',5'-cyclohexadienyl) derivative, lanomycin, leinamycin, leptomycin, libanomycin, lincomycin, lomofungin, lysolipin, magnesidin, manumycin, melanomycin, methoxycarbonylmethylmonate, methoxycarbonylethylmonate, methoxycarbonylphenylmonate, methyl pseudomonate, methylmonate, microcin, mitomalcin, mocimycin, moenomycin, monoacetyl cladosporin, monomethyl cladosporin, mupirocin, mupirocin calcium, mycobacidin, myriocin, myxopyronin, pseudoaglycone, nanaomycin, nancimycin, nargenicin, neocarcinostatin, neoenactin, neothramycin, nifurtoinol, nocardicin, nogalamycin, novobiocin, octylmonate, olivomycin, orthosomycin, oudemansin, oxirapentyn, oxoglaucine methiodide, pactacin, pactamycin, papulacandin, paulomycin, phaeoramularia fungicide, phenelfamycin, phenyl, cerulenin, phenylmonate, pholipomycin, pirlimycin, pleuromutilin, a polylactone derivative, polynitroxin, polyoxin, porfiromycin, pradimicin, prenomycin, prop-2-enylmonate, protomycin, Pseudomonas antibiotic, pseudomonic acid, purpuromycin, pyrinodemin, pyrroInitrin, pyrrolomycin, amino, chloro pentenedioic acid, rapamycin, rebeccamycin, resistomycin, reuterin, reveromycin, rhizocticin, roridin, rubiflavin, naphthyridinomycin, saframycin, saphenamycin, sarkomycin, sarkomycin, sclopularin, selenomycin, siccanin, spartanamicin, spectinomycin, spongistatin, stravidin, streptolydigin, Streptomyces arenae antibiotic complex, streptonigrin, streptothricins, streptovitacin, streptozotocine, a strobilurin derivative, stubomycin, sulfamethoxazol-trimethoprim, sakamycin, tejeramycin, terpentecin, tetrocarcin, thermorubin, thermozymocidin, thiamphenicol, thioaurin, thiolutin, thiomarinol, thiomarinol, tirandamycin, tolytoxin, trichodermin, trienomycin, trimethoprim, trioxacarcin, tyrissamycin, umbrinomycin, unphenelfamycin, urauchimycin, usnic acid, uredolysin, variotin, vermisporin, verrucarin and analogs, salts and derivatives thereof.

[0235] In one or more disclosures, the antibiotic agent is a naturally occurring antibiotic compound. As used herein, the term "naturally-occurring antibiotic agent" includes all antibiotics that are obtained, derived or extracted from plant or vertebrate sources. Non-limiting examples of families of naturally-occurring antibiotic agents include phenol, resorcinol, antibiotic aminoglycosides, anamycin, quinines, anthraquinones, antibiotic glycopeptides, azoles, macrolides, avilamycin, agropyrene, cnicin, aucubin antibioticsaponin fractions, berberine (isoquinoline alkaloid), arctiopicrin (sesquiterpene lactone), lupulone, humulone (bitter acids), allicin, hyperforin, echinacoside, coniosetin, tetramic acid, imanine and novoimanine.

[0236] Ciclopirox and ciclopiroxolamine possess fungicidal, fungistatic and sporicidal activity. They are active against a broad spectrum of dermatophytes, yeasts, molds and other fungi, such as Trichophytons species, Microsporum species, Epidermophyton species and yeasts (Candida albicans, Candida glabrata, other candida species and Cryptococcus neoformans). Some Aspergillus species are sensitive to ciclopirox as are some Penicillium. Likewise, ciclopirox is effective against many Gram-positive and Gram-negative bacteria (e.g., Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa, Staphylococcus and Streptococcus species), as well as Mycoplasma species, Trichomonas vaginalis and Actinomyces.

[0237] Plant oils and extracts which contain antibiotic agents are also useful. Non-limiting examples of plants that contain agents include thyme, Perilla, lavender, tea tree, Terfezia clayeryi, Micromonospora, Putterlickia verrucosa, Putterlickia pyracantha, Putterlickia retrospinosa, Maytenus ilicifolia, Maytenus evonymoides, Maytenus aquifolia, Faenia interjecta, Cordyceps sinensis, couchgrass, holy thistle, plantain, burdock, hops, echinacea, buchu, chaparral, myrrh, red clover and yellow dock, garlic, and St. John's wort. Mixtures of the antibiotic agents as described herein may also be employed.

[0238] Antimicrobial susceptibility testing using the methods and compositions described herein is particularly advantageous in selecting adequate antimicrobials for the treatment of GI tract infections and SIBO. For example, some bacterial strains isolated from subjects having SIBO have been identified as being resistant to common antibiotics (see, e.g., Bouhnik et al. (1999) Amer. J. Gastroenterol. 94(5): 1327-31). Thus, antimicrobial susceptibility testing using the methods described herein can be used to select adequate antibiotic regimens and dosing for the treatment of SIBO.

[0239] In some disclosures of any of the methods described herein, a subject identified as having SIBO or a SIBO-related condition is administered a pharmaceutical formulation comprising at least one antimicrobial (e.g., an antibiotic provided herein). Dosing of the antimicrobial may be adjusted depending on bacterial and / or archaeal load (e.g., bacterial load in the small intestine of a subject) and / or the types of bacteria / archaea identified in the GI tract of the subject or in a portion (e.g., the jejunum) of the GI tract of the subject. In some disclosures, the at least one antimicrobial is selected from the group consisting of a cephalosporin, a quinolone, tetracycline, ampicillin, erythromycin, rifaximin, metronidazole, erythromycin, amoxicillin-clavulanic acid, cefoxitin, ciprofloxacin, norfloxacin, neomycin, doxycycline, lincomycin, chloramphenicol, a carbopenem (e.g., ertapenem, doripenem, and meropenem), ceftriaxone, piperacillin, and tazobactam.

[0240] For example, a subject identified as having SIBO (or a SIBO-related condition) that includes a bacterial overgrowth of one or more of strains of Escherichia coli, Klebsiella spp., Enterobacter spp., Enterococcus faecalis, Enterococcus faecium, and Staphylococcus aureus may be administered a pharmaceutical formulation comprising rifaximin.

[0241] In some disclosures, the at least one antimicrobial is selected from the group consisting of meropenem, ceftriaxone, ertapenem, and piperacillin-tazobactam. In a related disclosure, the antimicrobial is indicated for the treatment of symptomology suggestive of SIBO.

[0242] A subject identified as having SIBO (or a SIBO-related condition) that includes a bacterial overgrowth of one or more of Staphylococcus aureus, Escherichia coli, Bacteroides fragilis, Streptococcus agalactiae, Haemophilus influenza, Bacteroides disasonis, Streptococcus pneumoniae, Klebsiella pneumoniae, Bacteroides ovatus, Streptococcus pyogenes, Moraxella catarrhalis, Bacteroides thetaiotaomicron, Proteus mirabilis, Bacteroides uniformis, Clostridium clostridioforme, Eubacterium lentum, Peptostreptococcus spp., Porphyromonas asaccharolytica, Prevotella bivia, Streptococcus pneumoniae, Citrobacter freundii, Clostridium perfringens, Staphylococcus epidermidis, Citrobacter koseri, Fusobacterium spp., Enterobacter aerogenes, Bacteroides vulgatus, Enterobacter cloacae, Haemophilus influenzae, Haemophilus parainfluenzae, Klebsiella oxytoca, Morganella morganii, Proteus vulgaris, Providencia stuartii, Providencia rettgeri , and Serratia marcescens may be administered a pharmaceutical formulation comprising ertapenem.

[0243] A subject identified as having SIBO (or a SIBO-related condition) that includes a bacterial overgrowth of one or more of Staphylococcus aureus, Escherichia coli, Bacteroides fragilis, Streptococcus agalactiae, Haemophilus influenza, Bacteroides thetaiotaomicron, Streptococcus pneumoniae, Klebsiella pneumoniae, Clostridium clostridioforme, Streptococcus pyogenes, Neisseria meningitides, Enterococcus faecalis, Proteus mirabilis, Peptostreptococcus spp., Viridans group streptococci, Pseudomonas aeruginosa, Streptococcus pneumoniae, Citrobacter freundii, Bacteroides distasonis, Staphylococcus epidermidis, Citrobacter diversus, Bacteroides ovatus, Acinetobacter spp., Bacteroides uniformis, Campylobacter jejuni, Bacteroides urolyticus, Aeromonas hydrophilia, Bacteroides vulgatus, Enterobacter cloacae,. Clostridium difficile, Hafnia alvei, Clostridium perfringens, Haemophilus influenza, Eubacterium lentum, Moraxella catarrhalis, Fusobacterium spp., Prevotella bivia, Klebsiella oxytoca, Prevotella intermedia, Morganella morganii, Prevotella melanogenica, Pasteurella multocida, Porphyomonas asaccharolytica, Proteus vulgaris, Propionibacterium acnes, Serratia marcescens, Salmonella spp., Shigella spp., and Yersinia enterocolitica may be administered a pharmaceutical formulation comprising meropenem.

[0244] A subject identified as having SIBO (or a SIBO-related condition) that includes a bacterial overgrowth of one or more of Staphylococcus aureus, Escherichia coli, Bacteroides fragilis, Haemophilus influenza, Bacteroides thetaiotaomicron, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Streptococcus pneumoniae, Serratia marcescens, Prevotella melanogenica, Staphylococcus epidermidis, Citrobacter koseri, Bacteroides distasonis, Enterococcus faecalis, Moraxella catarrhalis, Clostridium perfringens, Staphylococcus epidermidis, Morganella morganii, Streptococcus agalactiae, Proteus vulgaris, Streptococcus pneumoniae, Neisseria gonorrhoeae, Streptococcus pyogenes, Proteus mirabilis, Viridans group streptococci, Proteus vulgaris, Providencia stuartii, Providencia rettgeri, and Salmonella enterica may be administered a pharmaceutical formulation comprising piperacillin and tazobactam.

[0245] A subject identified as having SIBO (or a SIBO-related condition) that includes a bacterial overgrowth of one or more of Staphylococcus aureus, Escherichia coli, Bacteroides fragilis, Staphylococcus epidermidis, Haemophilus influenza, Clostridium spp., Streptococcus pneumoniae, Haemophilus parainfluenzae, Peptostreptococcus spp., Streptococcus pyogenes, Acinetobacter baumannii, Viridans group streptococci, Pseudomonas aeruginosa, Acinetobacter calcoaceticus, Enterobacter aerogenes, Klebsiella pneumoniae, Kelbsiella oxytoca, Moraxella catarrhalis, Morganella morganii, Neisseria gonorrhoeae, Neisseria meningitides, Proteus mirabilis, Proteus vulgaris, Serratia marcescens, Streptococcus agalactiae, Citrobacter diversus, Prevotella bivius, Citrobacter freundii, Bacteroides melanogenicus, Providencia spp. (e.g., Providencia rettgeri), and Salmonella spp. may be administered a pharmaceutical formulation comprising ceftriaxone.Methods of Selecting and Optimizing Treatment

[0246] The methods described herein include the administration of one or more treatments, i.e. antibiotics, to a subject identified as having or being at risk of developing SIBO. The methods can also include selecting a treatment for a subject who has SIBO or is determined to be at risk for developing SIBO, based upon the presence or absence of an analyte (e.g., a particular microorganism), or based upon the amount of an analyte.

[0247] The methods can also include administering a treatment (e.g., a pharmaceutical formulation including at least one therapeutic agent) selected by a method described herein to a subject who has or is at risk of developing SIBO to treat, delay disease progression, or reduce the risk of developing of the disease. In some embodiments, the formulation is comprised in an ingestible device as disclosed herein. In some embodiments wherein the formulation is comprised in an ingestible device, the formulation may be suitable for oral administration. The formulation may be, for example, a solid dosage form or a liquid dosage form. In some embodiments, the formulation is suitable for introduction and optionally for storage in an ingestible device described herein. In some embodiments, the formulation is suitable for introduction and optionally for storage in a reservoir comprised in the ingestible device. In some embodiments, the formulation is suitable for introduction and optionally for storage in the reservoir comprised in the ingestible device.

[0248] In some disclosures of any of the methods described herein, a subject having SIBO is administered an ingestible device (e.g., an ingestible device as described herein), wherein the device comprises a pharmaceutical formulation that is released at a location in the gastrointestinal tract of the subject. In some disclosures, the pharmaceutical formulation is released at a location in the gastrointestinal tract of the subject proximate to one or more sites of disease. In some embodiments, the pharmaceutical formulation comprises a therapeutic agent (e.g., a therapeutic agent described herein), and a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutical formulation is a personalized treatment for SIBO in the subject. In some embodiments, the ingestible device is configured to release the therapeutic agent according to desired (e.g., customized or optimized) dosage, timing, and / or location parameter.

[0249] Alternatively, the methods described herein can include administering a pharmaceutical formulation comprising a therapeutic agent (e.g., an antibiotic) in a suitable dosage form. The pharmaceutical formulation can be adapted for the chosen route of administration, e.g., orally or parenterally, or by intravenous, intramuscular, topical or subcutaneous routes. In some disclosures, for oral administration, the compounds can be formulated as a solid dosage form with or without an enteric coating.

[0250] The methods described herein include orally administering an effective amount of a pharmaceutical formulation comprising an antimicrobial agent (e.g., meropenem, ceftriaxone, ertapenem, or piperacillin-tazobactam) to a subject having SIBO. The pharmaceutical formulation may include a pharmaceutically acceptable vehicle such as an inert diluent, excipient or an assimilable edible carrier. Suitable dosage forms include hard or soft shell gelatin capsules, ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, and the like.

[0251] The amount of active compound in the pharmaceutical formulation is such that an effective dosage level will be obtained.

[0252] Appropriate excipients for tablets, troches, pills, capsules, and the like include: binders such as gum tragacanth, acacia, corn starch or gelatin; excipients such as dicalcium phosphate; a disintegrating agent such as corn starch, potato starch, alginic acid and the like; a lubricant such as magnesium stearate; and a sweetening agent such as sucrose, fructose, lactose or aspartame or a flavoring agent such as peppermint, oil of wintergreen, or cherry flavoring may be added. When the unit dosage form is a capsule, it may contain, in addition to materials of the above type, a liquid carrier, such as a vegetable oil or a polyethylene glycol. Various other materials may be present as coatings or to otherwise modify the physical form of the solid unit dosage form. For instance, tablets, pills, or capsules may be coated with gelatin, wax, shellac or sugar and the like. A syrup or elixir may contain the therapeutic agent, sucrose or fructose as a sweetening agent, methyl and propylparabens as preservatives, a dye and flavoring such as cherry or orange flavor. In addition, the therapeutic agent may be incorporated into sustained-release preparations, particles, and devices.

[0253] Pharmaceutical formulations comprising a therapeutic agent (e.g., an antibiotic) may also be administered intravenously or intramuscularly by infusion or injection. Solutions of the therapeutic agent or its salts can be prepared in water, optionally mixed with a nontoxic surfactant. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, triacetin, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these formulations contain a preservative to prevent the growth of microorganisms. Pharmaceutically acceptable excipients and dosage forms are described, for example, in In Remington: The Science and Practice of Pharmacy, 21st edition, 2005, ed. D. B. Troy, Lippincott Williams & Wilkins, Philadelphia; Encyclopedia of Pharmaceutical Technology, eds. J. Swarbrick and J. C. Boylan, 1988-1999, Marcel Dekker, New York; and Handbook of Pharmaceutical Excipients, 3rd Edition (2000) edited by A. H. Kibbe, American Pharmaceutical Association and Pharmaceutical Press.

[0254] Also provided herein are methods of determining the efficacy of SIBO treatment. In some embodiments, providing an ingestible device can determine successful treatment of SIBO in a subject (e.g., the presence or absence of an analyte is determined; the levels of an analyte is decreased as compared to the levels of the analyte determined in the subject at an early period of time; the levels of an analyte is decreased as compared to the levels of the analyte determined in a control subject (e.g., a subject that does not have SIBO, or is not at risk of developing SIBO); the levels of an analyte is increased as compared to the levels of the analyte determined in the subject at an early period of time). In some embodiments, prior to the providing an ingestible device step, the subject received treatment for SIBO (e.g., any of the treatment described herein). For example, in some embodiments, the level of an analyte (e.g., any of the analytes described herein) is decreased as compared to the level of the analyte described herein prior to treatment for SIBO, and further treatment is discontinued. For example, in some embodiments, the level of an analyte (e.g., any of the analytes described herein) is increased as compared to the level of the analyte described herein prior to treatment for SIBO, and a different treatment is administered.

[0255] Non-limiting examples of therapeutic agents for treating or preventing SIBO include substances that suppress cytokine production, downregulate or suppress self-antigen expression, or mask MHC antigens, and medical foods. Examples of such agents include 2-amino-6-aryl-5 -substituted pyrimidines (see U.S. Patent No. 4,665,077); non-steroidal anti-inflammatory drugs (NSAIDs); ganciclovir; tacrolimus; glucocorticoids such as Cortisol or aldosterone; anti-inflammatory agents such as a cyclooxygenase inhibitor; a 5-lipoxygenase inhibitor; or a leukotriene receptor antagonist; purine antagonists such as azathioprine or mycophenolate mofetil (MMF); alkylating agents such as cyclophosphamide; bromocryptine; danazol; dapsone; glutaraldehyde (which masks the MHC antigens, as described in U.S. Patent No. 4,120,649); anti-idiotypic antibodies for MHC antigens and MHC fragments; cyclosporine; 6-mercaptopurine; steroids such as corticosteroids or glucocorticosteroids or glucocorticoid analogs, e.g., prednisone, methylprednisolone, including SOLU-MEDROL ®< , methylprednisolone sodium succinate, and dexamethasone; dihydrofolate reductase inhibitors such as methotrexate (oral or subcutaneous); anti-malarial agents such as chloroquine and hydroxychloroquine; sulfasalazine; leflunomide; cytokine or cytokine receptor antibodies or 5 antagonists including anti-interferon-alpha, -beta, or -gamma antibodies, anti-tumor necrosis factor(TNF)-alpha antibodies (infliximab (REMICADE ®< ) or adalimumab), anti-TNF-alpha immunoadhesin (etanercept), anti-TNF-beta antibodies, anti-interleukin-2 (IL-2) antibodies and anti-IL-2 receptor antibodies, and anti-interleukin-6 (IL-6) receptor antibodies and antagonists; anti-LFA-1 antibodies, including anti-CD 1 la and anti-CD 18 antibodies; anti-L3T4 antibodies; heterologous anti-lymphocyte globulin; pan-T antibodies, anti-CD3 or anti-CD4 / CD4a antibodies; soluble peptide containing a LFA-3 binding domain (WO 90 / 08187 published Jul. 26, 1990); streptokinase; transforming growth factor-beta (TGF-beta); streptodomase; RNA or DNA from the host; FK506; RS-61443; chlorambucil; deoxyspergualin; rapamycin; T-cell receptor (Cohen et al., U.S. Patent No. 5,114,721); T-cell receptor fragments (Offner et al., Science, 251:430-432 (1991); WO 90 / 11294; Janeway, Nature, 341:482 (1989); and WO 91 / 01133); BAFF antagonists such as BAFF or BR3 antibodies or immunoadhesins and zTNF4 antagonists (for review, see Mackay and Mackay, Trends Immunol., 23:113-5 (2002); biologic agents that interfere with T cell helper signals, such as anti-CD40 receptor or anti-CD40 ligand (CD 154), including blocking antibodies to CD40-CD40 ligand (e.g., Durie et al., Science, 261:1328-30 (1993); Mohan et al., J. Immunol., 154:1470-80 (1995)) and CTLA4-Ig (Finck et al., Science, 265:1225-7 (1994)); and T-cell receptor antibodies (EP340,109) such as T10B9. Non-limiting examples of adjunct agents also include the following: budesonide; epidermal growth factor; aminosalicylates; metronidazole; mesalamine; olsalazine; balsalazide; antioxidants; thromboxane inhibitors; IL-1 receptor antagonists; anti-IL-1 monoclonal antibodies; growth factors; elastase inhibitors; pyridinylimidazole compounds; TNF antagonists; IL-4, IL-10, IL-13 and / or TGFβ cytokines or agonists thereof (e.g., agonist antibodies); IL-11; glucuronide- or dextran-conjugated prodrugs of prednisolone, dexamethasone or budesonide; ICAM-I antisense phosphorothioate oligodeoxynucleotides (ISIS 2302; Isis Pharmaceuticals, Inc.); soluble complement receptor 1 (TPlO; T Cell Sciences, Inc.); slow-release mesalazine; antagonists of platelet activating factor (PAF); ciprofloxacin; and lignocaine. As disclosed herein, the agents for treating or preventing SIBO include any antibiotic described herein (e.g., rifaximin). Examples of agents for UC are sulfasalazine and related salicylate-containing drugs for mild cases and corticosteroid drugs in severe cases.

[0256] Topical administration of either salicylates or corticosteroids is sometimes effective, particularly when the disease is limited to the distal bowel, and is associated with decreased side effects compared with systemic use. Supportive measures such as administration of iron and antidiarrheal agents are sometimes indicated. Azathioprine, 6-mercaptopurine and methotrexate are sometimes also prescribed for use in refractory corticosteroid-dependent cases.

[0257] Non-limiting examples of common therapeutic agents for the treatment of IBS-C, IB S-D, and bile acid diarrhea, as well as exemplary dosing regimens, are provided in the table below: Name Mechanism Dose IBS-CLinaclotide (Linzess, Constella)peptide agonist of the guanylate cyclase 2C. Reduces activation of colonic sensory neurons, reducing pain; and activates colonic motor neurons, which increases smooth muscle contraction and thus promotes bowel movements.290 mcg PO QDLubiprostone (Amitiza)Lubiprostone is a bicyclic fatty acid derived from prostaglandin E1 that acts by specifically activating ClC-2 chloride channels on the apical aspect of gastrointestinal epithelial cells, producing a chloride-rich fluid secretion. These secretions soften the stool, increase motility, and promote spontaneous bowel movements (SBM).8 mcg PO BIDLaxativesIBS-DRifaximin (Xifaxin)Antibiotic550 mg PO TID x 14 daysEluxadoline (Viberzi)Opioid receptor agonist100 mg PO BIDAlonsetron (Lontronex)Antagonist action on the 5-HT3 receptors of the enteric nervous system of the gastrointestinal tract0.5-1 mg PO BIDLoperamide (Imodium)Opioid-receptor agonistBile acid diarrheaCholestyramine, colestipol (Questran)4-8 g PO BID

[0258] In some embodiments of any of the methods described herein, a subject may be administered more than one ingestible device. For example, in some embodiments, a subject is administered a first ingestible device and a second ingestible device. In some embodiments, the subject is administered a first, a second, and a third ingestible device. In some embodiments, a subject is administered more than three ingestible devices (either concurrently or consecutively). Each ingestible device administered to a subject may have a different or the same function. For example, in some embodiments, a first ingestible device is suitable for monitoring, identifying and / or characterizing an analyte, and a second ingestible device is suitable for the delivery of a therapeutic agent (e.g., a therapeutic agent described herein). In some embodiments, a first ingestible device is suitable for collecting a sample from the gastrointestinal tract of a subject, and a second ingestible device is suitable for the delivery of a therapeutic agent. In some embodiments, a first ingestible device is suitable for collecting a sample from the gastrointestinal tract of a subject, and a second ingestible device is suitable for performing antimicrobial susceptibility / resistance analysis as described herein. A third ingestible device may be administered to a subject in order to monitor a disease state in the subject.

[0259] In some disclosures of any of the methods described herein, an ingestible device described herein is administered to a subject to collect a sample from the GI tract of a subject in order to monitor a level of a specific microorganism in the GI tract of the subject (e.g., before and after treatment with a therapeutic agent (e.g., an antimicrobial agent)).

[0260] The methods described herein include administering a treatment (e.g., an antibiotic) selected by a method described herein to a subject who has SIBO to treat, delay disease progression, or reduce the risk of developing the disease. An exemplary method for the diagnosis and treatment of SIBO is provided at FIG. 87. In some embodiments, a subject identified as having SIBO is administered an ingestible device described herein, wherein the device includes a sampling chamber. At least one sample may be collected from the GI tract of the subject (e.g., jejunal fluid) using the ingestible device. Sample(s) may be obtained from different regions of the GI tract of the subject (e.g., one or more of the duodenum, jejunum, ileum, ascending colon, transverse colon or descending colon). Upon excretion of the ingestible device from the subject, the sample(s) may be collected and analyzed as described herein the characterize one or more analytes (e.g., bacteria). Microbial isolates from the sample may be subjected to analysis to characterize the microbe and / or antimicrobial susceptibility testing may be performed to identify antimicrobial agents (e.g., cytostatic or cytolytic agents) that can be effectively used against the microbial isolates. The subject can then be administered a pharmaceutical formulation comprising the identified antimicrobial agent. The formulation may be administered using an ingestible device as disclosed herein or it may be administered by other means (e.g., intravenously, rectally, orally, etc.). The efficacy of treatment may be monitored as described herein to improve the antibiotic selection. Additionally, the subject may be administered one or more ingestible devices to monitor, identify and / or characterize methane levels, pH, temperature, and one or more metabolites in the GI tract of the subject.

[0261] Accordingly, in some dislosures, the methods described herein comprise (a) diagnosing a subject as having an overgrowth of bacteria in the gastrointestinal tract; wherein the step of diagnosing comprises use of an ingestible device; and (b) administering one of ertapenem, meropenem, ceftriaxone, and piperacillin-tazobactam based on the diagnosis of step (a).Methods Relating to Subjects Having Small Intestinal Bacterial Overgrowth (SIBO)

[0262] In an aspect, provided herein are methods for treating small intestinal bacterial overgrowth (SIBO) in a subject in need thereof, the method comprising: orally administering an effective amount of a pharmaceutical formulation comprising an antimicrobial agent to the subject, thereby treating SIBO in the subject, wherein the antimicrobial agent is meropenem or ceftriaxone.

[0263] In some embodiments, treating SIBO comprises ameliorating or decreasing the severity of one or more symptoms associated with SIBO. In some embodiments, the one or more symptoms associated with SIBO are selected from bloating, diarrhea, flatulence, increased or decreased stool frequency, abdominal pain, constipation, weight loss, fever, abdominal tenderness, nausea, gastric stasis, and steatorrhea.

[0264] In some embodiments, treating SIBO comprises partially eradicating the bacterial overgrowth of the small intestine.

[0265] In some embodiments, the method further comprises the step of identifying a subject having SIBO.

[0266] In some embodiments, identifying a subject having SIBO comprises obtaining a fluid sample from the small intestine and measuring the bacterial concentration, wherein a bacterial concentration of about 10 3< CFU / mL or greater in the fluid is indicative that the subject has small intestinal bacterial overgrowth (SIBO).

[0267] In some embodiments, identifying a subject having SIBO comprises obtaining a fluid sample from the small intestine and measuring the bacterial concentration, wherein a bacterial concentration of about 10 4< CFU / mL or greater in the fluid is indicative that the subject has small intestinal bacterial overgrowth (SIBO).

[0268] In some embodiments, identifying a subject having SIBO comprises obtaining a fluid sample from the small intestine and measuring the bacterial concentration, wherein a bacterial concentration of about 10 5< CFU / mL or greater in the fluid is indicative that the subject has small intestinal bacterial overgrowth (SIBO).

[0269] In some embodiments, identifying a subject having SIBO comprises measuring an amount of hydrogen or methane, or both, in the breath of a subject after the subject has consumed a substrate selected from the group consisting of lactulose, xylose, lactose, and glucose, wherein an amount of hydrogen or methane, or both, that exceeds a normal range of hydrogen or methane, or both, is indicative that the subject has SIBO.

[0270] In some embodiments, an effective amount of the antimicrobial for the treatment SIBO is from about one-quarter to about two-times of a standard dose of the antimicrobial. A standard dose is that regularly used by clinicians for the treatment of other types of infection, and can be informed by the dosing included in, e.g., an FDA label.

[0271] As described herein, the antimicrobial is meropenem or ertapenem and the antimicrobial is co-administered with one or more carbapenemase inhibitors. In some embodiments, the carbapenemase inhibitor is selected from sulbactam tazobactam, clavulanic acid, avibactam, and vaborbactam. In some embodiments, the carbapenemase inhibitor is selected from relebactam, a boronic acid-based inhibitor (e.g., PRX7009), a b-lactamase inhibitory protein II, and Zinc01807204 and Zinc02318494 compounds. In some embodiments, the carbapenemase inhibitor is a metallo-b-lactamase inhibitor selected from EDTA, thioester derivatives, propionic acid, maleic acid, succinic acid and phthalic acid derivatives.

[0272] In some embodiments, the method of treating SIBO further comprises administering intestinal lavage or enema to the subject.

[0273] In some embodiments, the method of treating SIBO further comprises administering a probiotic to the subject.

[0274] In some embodiments, the method of treating SIBO further comprises modifying the subject's diet. In some embodiments, modifying a subject' diet comprises increasing the subject's consumption of dietary fiber.

[0275] In some embodiments, the method of treating SIBO further comprises administering a chemical prokinetic agent to the subject. Non-limiting examples of prokinetic agents include motilin or functional analogues thereof, a macrolide compound such as erythromycin or azithromycin, or a bile acid, or a bile salt derived therefrom. Example bile acids include ursodeoxycholic acid and chenodeoxycholic acid, and their pharmaceutically acceptable salts (e.g., sodium or potassium salts). Other prokinetic agents are compounds with cholinergic activity such as cisapride. Other prokinetic agents are dopamine antagonists such as metoclopramide, domperidone, or bethanechol.

[0276] In some embodiments, the method of treating SIBO further comprises administering bile acid replacement therapy to the subject.

[0277] In some embodiments, the method of treating SIBO further comprises administering a nitric oxide altering agent such as nitroglycerin, N-omega-nitro-L-arginine methylester (L-NAME), N-monomethyl-L-arginine (L-NMMA), or a 5-hydroxytryptamine (HT or serotonin) receptor antagonist, such as ondansetron or alosetron to the subject.

[0278] In some embodiments, the method of treating SIBO further comprises administering an antihistamine to the subject. Suitable antihistamines include, but are not limited to, promethazine and meclizine.

[0279] In some embodiments, the method of treating SIBO further comprises administering a neuroleptic agent to the subject. Suitable neuroleptic agents include, but are not limited to, prochlorperazine, chlorpromazine, or haloperidol.

[0280] In some embodiments, the method of treating SIBO further comprises administering a kappa agonist (e.g., fedotozine) to the subject.

[0281] In some embodiments, the method of treating SIBO further comprises administering an anti-inflammatory cytokine or an agonist thereof, substantially simultaneously with or after at least partially eradicating the bacterial overgrowth of the small intestine to further ameliorate the symptoms of SIBO. Anti-inflammatory cytokines include human IL-4, IL- 10, IL-11, or TGF-β, derived from a human source or a transgenic non-human source expressing a human gene. The anti-inflammatory cytokine is injected or infused intravenously or subcutaneously.

[0282] In some embodiments, the method of treating SIBO further comprises administering a pro-inflammatory cytokine or an antibody that specifically binds a pro-inflammatory cytokine substantially simultaneously with or after at least partially eradicating the bacterial overgrowth of the small intestine to further ameliorate the symptoms of SIBO. The antagonist or antibody is one that binds to a pro-inflammatory cytokine or antagonizes the activity or receptor binding of a pro inflammatory cytokine. Pro-inflammatory cytokines include TNF-α, IL-1α, IL-1β, IL-6, IL-8, IL-12, or LIF. The cytokine antagonist or antibody can be derived from a human source or is a chimeric protein having a human protein constituent. The cytokine antagonist or antibody can be delivered to the human subject by intravenous infusion.

[0283] In some embodiments, the method of treating SIBO further comprises administering an agent that modifies afferent neural feedback or sensory perception. Agents that modify afferent neural feedback or sensory perception include 5-HT receptor antagonists, such as ondansetron and alosetron; opiate agonists, such as fedotozine; peppermint oil; cisapride; a dopamine antagonist, such as domperidone; an antidepressant agent; an anxiolytic agent; or a combination of any of these. Useful antidepressant agents include tricyclic antidepressants, such as amitriptyline (Elavil); tetracyclic antidepressants, such as maprotiline; serotonin re-uptake inhibitors, such as fluoxetine (Prozac) or sertraline (Zoloft); monoamine oxidase inhibitors, such as phenezline; and miscellaneous antidepressants, such as trazodone, venlafaxine, mirtazapine, nefazodone, or bupropion (Wellbutrin). Typically, useful antidepressant agents are available in hydrochloride, sulfated, or other conjugated forms, and all of these conjugated forms are included among the useful antidepressant agents. Useful anxiolytic (anti-anxiety) agents include benzodiazepine compounds, such as Librium, Atavin, Xanax, Valium, Tranxene, and Serax, or other anxiolytic agents such as Paxil.

[0284] In some embodiments, SIBO is refractory (e.g., not responsive to prior, different course of treatment).

[0285] In some embodiments, SIBO is relapsed (e.g., progresses at the conclusion of a prior, different course of treatment).

[0286] In another aspect, provided herein are methods for treating SIBO, the method comprising orally administering an effective amount of a pharmaceutical formulation comprising an antimicrobial agent to the subject, wherein the antimicrobial agent exhibits antimicrobial activity against a bacterium implicated in the pathogenesis of SIBO, thereby treating SIBO in the subject.

[0287] In some embodiments, the antimicrobial agent exhibits antimicrobial activity against a bacterium implicated in the pathogenesis of SIBO. In some embodiments, the antimicrobial agent exhibits antimicrobial activity against the bacterium with a minimal inhibitory concentration (MIC) range of less than about 0.001 µg / mL to greater than about 128 µg / mL, such as about 0.001 µg / mL to about 128 µg / mL, about 0.001 µg / mL to about 64 µg / mL, about 0.001 µg / mL to about 32 µg / mL, about 0.001 µg / mL to about 16 µg / mL, about 0.001 µg / mL to about 8 µg / mL, about 0.001 µg / mL to about 4 µg / mL, about 0.001 µg / mL to about 2 µg / mL, about 0.001 µg / mL to about 1 µg / mL, about 0.001 µg / mL to about 0.5 µg / mL, about 0.001 µg / mL to about 0.3 µg / mL, about 0.001 µg / mL to about 0.15 µg / mL, about 0.001 µg / mL to about 0.1 µg / mL, about 0.001 µg / mL to about 0.05 µg / mL, about 0.001 µg / mL to about 0.015 µg / mL, about 0.015 µg / mL to about 128 µg / mL, about 0.015 µg / mL to about 64 µg / mL, about 0.015 µg / mL to about 32 µg / mL, about 0.015 µg / mL to about 16 µg / mL, about 0.015 µg / mL to about 8 µg / mL, about 0.015 µg / mL to about 4 µg / mL, about 0.015 µg / mL to about 2 µg / mL, about 0.015 µg / mL to about 1 µg / mL, about 0.015 µg / mL to about 0.5 µg / mL, about 0.015 µg / mL to about 0.3 µg / mL, about 0.015 µg / mL to about 0.15 µg / mL, about 0.015 µg / mL to about 0.1 µg / mL, about 0.015 µg / mL to about 0.05 µg / mL, about 0.03 µg / mL to about 128 µg / mL, about 0.03 µg / mL to about 64 µg / mL, about 0.03 µg / mL to about 32 µg / mL, about 0.03 µg / mL to about 16 µg / mL, about 0.03 µg / mL to about 8 µg / mL, about 0.03 µg / mL to about 4 µg / mL, about 0.03 µg / mL to about 2 µg / mL, about 0.03 µg / mL to about 1 µg / mL, about 0.03 µg / mL to about 0.5 µg / mL, about 0.03 µg / mL to about 0.3 µg / mL, about 0.03 µg / mL to about 0.15 µg / mL, about 0.03 µg / mL to about 0.1 µg / mL, about 0.03 µg / mL to about 0.05 µg / mL, about 0.12 µg / mL to about 128 µg / mL, about 0.12 µg / mL to about 64 µg / mL, about 0.12 µg / mL to about 32 µg / mL, about 0.12 µg / mL to about 16 µg / mL, about 0.12 µg / mL to about 8 µg / mL, about 0.12 µg / mL to about 4 µg / mL, about 0.12 µg / mL to about 2 µg / mL, about 0.12 µg / mL to about 1 µg / mL, about 0.12 µg / mL to about 0.5 µg / mL, about 0.12 µg / mL to about 0.3 µg / mL, about 0.12 µg / mL to about 0.15 µg / mL, about 0.5 µg / mL to about 128 µg / mL, about 0.5 µg / mL to about 64 µg / mL, about 0.5 µg / mL to about 32 µg / mL, about 0.5 µg / mL to about 16 µg / mL, about 0.5 µg / mL to about 8 µg / mL, about 0.5 µg / mL to about 4 µg / mL, about 0.5 µg / mL to about 2 µg / mL, about 0.5 µg / mL to about 1 µg / mL, about 1 µg / mL to about 128 µg / mL, about 1 µg / mL to about 64 µg / mL, about 1 µg / mL to about 32 µg / mL, about 1 µg / mL to about 16 µg / mL, about 1 µg / mL to about 8 µg / mL, about 1 µg / mL to about 4 µg / mL, about 1 µg / mL to about 2 µg / mL, about 2 µg / mL to about 128 µg / mL, about 2 µg / mL to about 64 µg / mL, about 2 µg / mL to about 32 µg / mL, about 2 µg / mL to about 16 µg / mL, about 2 µg / mL to about 8 µg / mL, about 2 µg / mL to about 4 µg / mL, about 4 µg / mL to about 128 µg / mL, about 4 µg / mL to about 64 µg / mL, about 4 µg / mL to about 32 µg / mL, about 4 µg / mL to about 16 µg / mL, about 4 µg / mL to about 8 µg / mL, about 8 µg / mL to about 128 µg / mL, about 8 µg / mL to about 64 µg / mL, about 8 µg / mL to about 32 µg / mL, or about 8 µg / mL to about 16 µg / mL. In some embodiments, the antimicrobial agent exhibits antimicrobial activity against the bacterium with a MIC range of about 0.002 µg / mL to about 0.5 µg / mL, about 0.002 µg / mL to about 128 µg / mL, about 0.008 µg / mL to about 0.3 µg / mL, about 0.008 µg / mL to about 1 µg / mL, about 0.008 µg / mL to about 2 µg / mL, about 0.008 µg / mL to about 8 µg / mL, about 0.008 µg / mL to about 128 µg / mL, about 0.015 µg / mL to 2 about 0.015 µg / mL to 128 µg / mL, about 0.03 µg / mL to about 8 µg / mL, about 0.03 µg / mL to about 64 µg / mL, about 0.06 µg / mL to about 2 µg / mL, about 0.06 µg / mL to about 16 µg / mL, about 0.12 µg / mL to about 8 µg / mL, about 0.12 µg / mL to about 128 µg / mL, about 0.5 µg / mL to about 16 µg / mL, about 0.5 µg / mL to about 128 µg / mL, about 1 µg / mL to about 64 µg / mL, about 1 µg / mL to about 128 µg / mL, about 2 µg / mL to about 64 µg / mL, about 4 µg / mL to about 128 µg / mL, or about 8 µg / mL to about 128 µg / mL. In some embodiments, the antimicrobial agent exhibits antimicrobial activity against the bacterium with a MIC range of about 0.001 µg / mL to about 128 µg / mL, about 0.001 µg / mL to about 64 µg / mL, about 0.004 µg / mL to about 32 µg / mL, about 0.015 µg / mL to about 16 µg / mL, about 0.03 µg / mL to about 8 µg / mL, or about 0.5 µg / mL to about 2 µg / mL. In some embodiments, the antimicrobial agent is meropenem. In some embodiments, the antimicrobial agent is ceftriaxone.

[0288] In some embodiments, the antimicrobial agent exhibits antimicrobial activity against the bacterium implicated in the pathogenesis of SIBO, with a MIC 50 value of less than about 0.001 µg / mL to greater than about 128 µg / mL, about 0.001 µg / mL to about 64 µg / mL, about 0.004 µg / mL to about 32 µg / mL, about 0.015 µg / mL to about 16 µg / mL, about 0.03 µg / mL to about 8 µg / mL, about 0.5 µg / mL to about 2 µg / mL, or about 0.001 µg / mL, about 0.002 µg / mL, about 0.004 µg / mL, about 0.015 µg / mL, about 0.03 µg / mL, about 0.06 µg / mL, about 0.12 µg / mL, about 0.25 µg / mL, about 0.5 µg / mL, about 1 µg / mL, about 4 µg / mL, about 8 µg / mL, about 16 µg / mL, about 32 µg / mL, about 64 µg / mL, or about 128 µg / mL. In some embodiments, the antimicrobial agent is meropenem. In some embodiments, the antimicrobial agent is ceftriaxone.

[0289] In some embodiments, the antimicrobial agent exhibits antimicrobial activity against the bacterium implicated in the pathogenesis of SIBO, with a MIC 90 value of less than about 0.001 µg / mL to greater than about 128 µg / mL, about 0.001 µg / mL to about 64 µg / mL, about 0.004 µg / mL to about 32 µg / mL, about 0.015 µg / mL to about 16 µg / mL, about 0.03 µg / mL to about 8 µg / mL, about 0.5 µg / mL to about 2 µg / mL, or about 0.001 µg / mL, about 0.002 µg / mL, about 0.008 µg / mL, about 0.015 µg / mL, about 0.03 µg / mL, about 0.06 µg / mL, about 0.12 µg / mL, about 0.25 µg / mL, about 0.5 µg / mL, about 2 µg / mL, about 4 µg / mL, about 8 µg / mL, about 16 µg / mL, about 32 µg / mL, about 64 µg / mL, or about 128 µg / mL. In some embodiments, the antimicrobial agent is meropenem. In some embodiments, the antimicrobial agent is ceftriaxone.

[0290] In some embodiments, the bacterium implicated in the pathogenesis of SIBO is selected from the group consisting of a gram-positive bacterium, a gram-negative bacterium, an anaerobic bacterium, and combinations thereof.

[0291] In some embodiments, the bacterium implicated in the pathogenesis of SIBO is a gram-negative bacterium. Examples of gram-negative bacterium implicated in the pathogenesis of SIBO include, but are not limited to, Enterobacter aerogenes, Escherichia coli, Klebsiella spp., for example, K. oxytoca and K. pneumonia, Proteus mirabilis, and Pseudomonas aeruginosa.

[0292] In some embodiments, the bacterium implicated in the pathogenesis of SIBO is a gram-positive bacterium. Examples of gram-positive bacterium implicated in the pathogenesis of SIBO include, but are not limited to, Staphylococcus aureus, Enterococcus faecalis, and Streptococcus spp., for example, Streptococcus pyogenes, Streptococcus agalactiae, and Viridans group Streptococcus.

[0293] In some embodiments, the bacterium implicated in the pathogenesis of SIBO is an anaerobic bacterium. Examples of anaerobic bacterium implicated in the pathogenesis of SIBO suggestive of SIBO include, but are not limited to, Clostridium spp., for example, C. sporogenes, C. ramosum, and C. innocuum, Prevotella spp., for example, P. melanogenica, P. bivia, P. buccae, P. nanceiensis, P. intermedia, P. denticola, P. nigrescens, P. corporis, P. bergensis, and P. disiens, Veillonella spp., for example, V. parvula, Veillonella dispr, and V. atypica, Bacteroides fragilis, and Bacteroides non-fragilis, for example, B. caccae, B. thetaiotaomicron, B. ovatus, B. vulgatus, B. uniformis, B. stercoris, B. xylanisolvens, B salyersiae, B. intestinalis, and B. faecis.

[0294] In some embodiments, the antimicrobial agent exhibits antimicrobial activity against a bacterium implicated in the pathogenesis of SIBO, where the bacterium is selected from the group consisting of Enterobacter aerogenes, Escherichia coli, Klebsiella spp., K. oxytoca, K. pneumonia, Proteus mirabilis, Pseudomonas aeruginosa, Staphylococcus aureus, Enterococcus faecalis, Streptococcus spp., Streptococcus pyogenes, Streptococcus agalactiae, Viridans group Streptococcus, Clostridium spp., C. sporogenes, C. ramosum, C. innocuum, Prevotella spp., P. melanogenica, P. bivia, P. buccae, P. nanceiensis, P. intermedia, P. denticola, P. nigrescens, P. corporis, P. bergensis, P. disiens, Veillonella spp., V. parvula, Veillonella dispr, V. atypica, Bacteroides fragilis, Bacteroides non-fragilis, B. caccae, B. thetaiotaomicron, B. ovatus, B. vulgatus, B. uniformis, B. stercoris, B. xylanisolvens, B salyersiae, B. intestinalis, and B. faecis. In some embodiments, the the antimicrobial agent is meropenem. In some embodiments, the antimicrobial agent is ceftriaxone.

[0295] In some embodiments, the antimicrobial agent exhibits bactericidal efficacy against a bacterium implicated in the pathogenesis of SIBO. For example, exposure of the bacterium to the antimicrobial agent for a period of time can result in reduction in colony forming units (CFU) per mL of the bacterium. In some embodiments, exposure of the bacterium to the antimicrobial agent for a period of time results in a reduction in CFU / mL of the bacterium of about 0.5-log to about 5-log or greater, such as about 0.5-log to about 4.5-log, about 0.5-log to about 4-log, about 0.5-log to about 3.5-log, about 0.5-log to about 3-log, about 0.5-log to about 2.5-log, about 0.5-log to about 2-log, about 0.5-log to about 1.5-log, about 0.5-log to about 1-log, about 1-log to about 5-log, about 1-log to about 4.5-log, about 1-log to about 4-log, about 1-log to about 3.5-log, about 1-log to about 3-log, about 1-log to about 2.5-log, about 1-log to about 2-log, about 1-log to about 1.5-log, about 1.5-log to about 5-log, about 1.5-log to about 4.5-log, about 1.5-log to about 4-log, about 1.5-log to about 3.5-log, about 1.5-log to about 3-log, about 1.5-log to about 2.5-log, about 1.5-log to about 2-log, about 2-log to about 5-log, about 2-log to about 4.5-log, about 2-log to about 4-log, about 2-log to about 3.5-log, about 2-log to about 3-log, about 2-log to about 2.5-log, about 2.5-log to about 5-log, about 2.5-log to about 4.5-log, about 2.5-log to about 4-log, about 2.5-log to about 3.5-log, about 2.5-log to about 3-log, about 3-log to about 5-log, about 3-log to about 4.5-log, about 3-log to about 4-log, about 3-log to about 3.5-log, about 3.5-log to about 5-log, about 3.5-log to about 4.5-log, about 3.5-log to about 4-log, about 4-log to about 5-log, about 4-log to about 4.5-log, about 4.5-log to about 5-log, or at least ≥0.5-log, ≥1-log, ≥1.5-log, ≥2-log, ≥2.5-log, ≥3-log, ≥3.5-log, ≥4-log, ≥4.5-log, ≥5-log, ≥6-log, ≥7-log, ≥8-log, ≥9-log, ≥10-log, or greater. In some embodiments, the antimicrobial agent exhibits bactericidal efficacy of at least a 3-log reduction in CFU / mL in about 1 hour, about 2 hours, about 4 hours, about 6 hours, about 8 hours, about 10 hours, about 12 hours, about 14 hours, about 16 hours, about 18 hours, about 20 hours, about 24 hours, about 30 hours, about 36 hours, about 42 hours, or about 48 hours. In some embodiments, the antimicrobial agent exhibits bactericidal efficacy of at least a 3-log reduction in CFU / mL in about 2 hours. In some embodiments, the antimicrobial agent exhibits bactericidal efficacy of at least a 3-log reduction in CFU / mL in about 6 hours. In some embodiments, the antimicrobial agent exhibits bactericidal efficacy of at least a 3-log reduction in CFU / mL in about 24 hours. In some embodiments, the bacterium is selected from E. coli, Streptococcus spp., and Bacteroides spp. In some embodiments, the the antimicrobial agent is meropenem. In some embodiments, the antimicrobial agent is ceftriaxone.

[0296] In some embodiments, the antimicrobial agent exhibits bactericidal efficacy against a bacterium implicated in the pathogenesis of SIBO at a concentration of about 0.5X MIC to about 8X MIC, such as about 0.5X MIC to about 6X MIC, about 0.5X MIC to about 4X MIC, about 0.5X MIC to about 2X MIC, about 0.5X MIC to about 1X MIC, about 1X MIC to about 8X MIC, about 1X MIC to about 6X MIC, about 1X MIC to about 4X MIC, about 1X MIC to about 2X MIC, about 2X MIC to about 8X MIC, about 2X MIC to about 6X MIC, about 2X MIC to about 4X MIC, about 4X MIC to about 8X MIC, about 4X MIC to about 6X MIC, about 6X MIC to about 8X MIC, or about 0.5X MIC, about 1X MIC, about 2X MIC, about 3X MIC, about 4X MIC, about 5X MIC, about 6X MIC, about 7X MIC, or about 8X MIC. In some embodiments, the the antimicrobial agent is meropenem. In some embodiments, the antimicrobial agent is ceftriaxone.

[0297] In some embodiments, exposure of the bacterium implicated in the pathogenesis of SIBO prevents regrowth of the bacterium. In some embodiments, the the antimicrobial agent is meropenem. In some embodiments, the antimicrobial agent is ceftriaxone.

[0298] In some embodiments, the antimicrobial agent is bacteriostatic with respect to one or more bacterium implicated in the pathogenesis of SIBO. "Bacteriostatic" refers to the ability of the antimicrobial agent to prevent or inhibit growth of a bacterium. In some embodiments, the antimicrobial agent is bactericidal with respect to one or more bacterium implicated in the pathogenesis of SIBO. "Bactericidal" refers to the ability of the antimicrobial agent to kill a bacterium. In some embodiments, the antimicrobial agent is both bacteriostatic and bactericidal with respect to one or more bacterium implicated in the pathogenesis of SIBO. In some embodiments, the bacterium is selected from E. coli, Streptococcus spp., and Bacteroides spp. In some embodiments, the the antimicrobial agent is meropenem. In some embodiments, the antimicrobial agent is ceftriaxone.

[0299] In some embodiments, the bacterium implicated in the pathogenesis of SIBO. For example, the bacterium can have a spontaneous mutation frequency of less than about 10 -7< , such as less than 10 -8< or 10 -9< , such as less than 1×10 -10< . In some embodiments, the bacterium has a spontaneous mutation frequency of less than about 7.45×10 -9< , about 5.75×10 -9< , about 5.15×10 -9< , about 9.55×10 -10< , about 1.85×10 -10< , about 1.75×10 -10< , about 1.50×10 -10< , or about 1.05×10 -10< . In some embodiments, the bacterium is selected from Escherichia coli, Streptococcus spp., S. pneumonia, S. pyogenes, S. agalactiae, Bacteroides spp., B. fragilis, B. vulgatus, and B. ovatus. In some embodiments, the the antimicrobial agent is meropenem. In some embodiments, the antimicrobial agent is ceftriaxone.

[0300] In some embodiments, the antimicrobial agent exhibits a mutation prevention concentration (MPC) of about 0.01 µg / mL to about 32 µg / mL, about 0.05 µg / mL to about 1 µg / mL, or about 0.1 µg / mL to about 0.25 µg / mL against the bacterium implicated in the pathogenesis of SIBO is unable to or is not susceptible to develop resistance to the antimicrobial agent, such as about 0.01 µg / mL to about 1 µg / mL, about 0.01 µg / mL to about 0.5 µg / mL, about 0.01 µg / mL to about 0.25 µg / mL, about 0.01 µg / mL to about 0.12 µg / mL, about 0.01 µg / mL to about 0.06 µg / mL, about 0.06 µg / mL to about 1 µg / mL, about 0.06 µg / mL to about 0.5 µg / mL, about 0.06 µg / mL to about 0.25 µg / mL, about 0.06 µg / mL to about 0.12 µg / mL, about 0.12 µg / mL to about 1 µg / mL, about 0.12 µg / mL to about 0.5 µg / mL, about 0.12 µg / mL to about 0.25 µg / mL, about 0.25 µg / mL to about 1 µg / mL, about 0.25 µg / mL to about 0.5 µg / mL, or about 0.5 µg / mL to about 1 µg / mL. In some embodiments, the MPC is about 0.03 µg / mL, about 0.06 µg / mL, about 0.12 µg / mL, about 0.25 µg / mL, about 0.5 µg / mL, or about 32 µg / mL. In some embodiments, the bacterium is selected from Escherichia coli, Streptococcus spp., S. pneumonia, S. pyogenes, S. agalactiae, Bacteroides spp., B. fragilis, B. vulgatus, and B. ovatus. In some embodiments, the the antimicrobial agent is meropenem. In some embodiments, the antimicrobial agent is ceftriaxone.Analytes

[0301] The compositions and methods described herein can be used to detect, analyze, and / or quantitate a variety of analytes in a human subject. "Analyte" as used in the present application refers to a compound or composition to be detected in a sample. Exemplary analytes suitable for use in the present application include those described in U.S. Patent 6,251,581. Broadly speaking, an analyte can be any substance (e.g., a substance with one or more antigens) capable of being detected. An exemplary and non-limiting list of analytes includes ligands, proteins and fragments thereof, blood clotting factors, hormones, cytokines, polysaccharides, nucleic acids, carbohydrates, mucopolysaccharides, lipids, fatty acids, microorganisms (e.g., bacteria), microbial antigens, and therapeutic agents (including fragments and metabolites thereof).

[0302] For instance, the analyte may be a substance that binds to an analyte-binding agent (e.g., a biomolecule) and forms a complex. In some disclosures, the analyte may be monovalent (monoepitopic) or polyvalent (polyepitopic), usually antigenic or haptenic. In some disclosures, the analyte is a single compound or plurality of compounds. In some disclosures, the analyte is a plurality of compounds which share at least one common epitopic or determinant site. The analyte can be a part of a cell such as bacteria or a cell bearing a blood group antigen such as A, B, D, etc., a human leukocyte antigen (HLA), or other cell surface antigen. The analyte can also be a microorganism (e.g., bacterium (e.g. a pathogenic bacterium), a fungus, protozoan, or a virus), a protein, a nucleic acid, a lipid, or a hormone. In some disclosures, the analyte can be an exosome or a part of an exosome (e.g., a bacterial exosome). In some disclosures, the analyte is derived from a subject (e.g., a human subject). In some disclosures, the analyte is derived from a microorganism present in the subject. In some disclosures, the analyte is a nucleic acid (e.g., a DNA molecule or a RNA molecule), a protein (e.g., a soluble protein, a cell surface protein), or a fragment thereof, that can be detected using any of the devices and methods provided herein.

[0303] The polyvalent ligand analytes will normally be poly(amino acids), e.g., a polypeptide (e.g., protein) or a peptide, polysaccharides, nucleic acids (e.g., DNA or RNA), and combinations thereof. Such combinations include components of bacteria, viruses, chromosomes, genes, mitochondria, nuclei, cell membranes, and the like.

[0304] In some disclosures, the polyepitopic ligand analytes have a molecular weight of at least about 5,000 Da, more usually at least about 10,000 Da. In the poly(amino acid) category, the poly(amino acids) of interest may generally have a molecular weight from about 5,000 Da to about 5,000,000 Da, more usually from about 20,000 Da to about 1,000,000 Da; among the hormones of interest, the molecular weights will usually range from about 5,000 Da to about 60,000 Da.

[0305] In some disclosures, the monoepitopic ligand analytes generally have a molecular weight of from about 100 to about 2,000 Da, more usually from about 125 to about 1,000 Da.

[0306] A wide variety of proteins may be considered as to the family of proteins having similar structural features, proteins having particular biological functions, proteins related to specific microorganisms, particularly disease causing microorganisms, etc. Such proteins include, for example, immunoglobulins, cytokines, enzymes, hormones, cancer antigens, nutritional markers, tissue specific antigens, etc.

[0307] In some disclosures, the analyte is a protein. In some disclosures, the analyte is a protein, e.g., an enzyme (e.g., a hemolysin, a protease, a phospholipase), a soluble protein, a membrane-bound protein, or an exotoxin. In some disclosures, the analyte is a fragment of a protein, a peptide, or an antigen. In some disclosures, the analyte is a peptide of at least 5 amino acids (e.g., at least 6, at least 7, at least 8, at least 9, at least 10, at least 25, at least, 50, or at least 100 amino acids). Exemplary lengths include 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 50, 75, or 100 amino acids. Exemplary classes of protein analytes include, but are not limited to: protamines, histones, albumins, globulins, scleroproteins, phosphoproteins, antibodies, affimers, mucoproteins, chromoproteins, lipoproteins, nucleoproteins, glycoproteins, T-cell receptors, proteoglycans, cell surface receptors, membrane-anchored proteins, transmembrane proteins, secreted proteins, HLA, and unclassified proteins. In some disclosures, the analyte is an affimer (see, e.g., Tiede et al. (2017) eLife 6:e24903).

[0308] Exemplary analytes include: Prealbumin, Albumin, α 1 -Lipoprotein, α 1 -Antitrypsin, α 1 -Glycoprotein, Transcortin, 4.6S-Postalbumin, α 1 -glycoprotein, α 1X -Glycoprotein, Thyroxin-binding globulin, Inter-α-trypsin-inhibitor, Gc-globulin (Gc 1-1, Gc 2-1, Gc 2-2), Haptoglobin (Hp 1-1, Hp 2-1, Hp 2-2), Ceruloplasmin, Cholinesterase, α 2 -Lipoprotein(s), Myoglobin, C-Reactive Protein, α 2 -Macroglobulin, α 2 -HS-glycoprotein, Zn-α 2 -glycoprotein, α 2 -Neuramino-glycoprotein, Erythropoietin, β-lipoprotein, Transferrin, Hemopexin, Fibrinogen, Plasminogen, β 2 -glycoprotein I, β 2 -glycoprotein II, Immunoglobulin G (IgG) or γG-globulin, Immunoglobulin A (IgA) or γA-globulin, Immunoglobulin M (IgM) or γM-globulin, Immunoglobulin D (IgD) or γD-Globulin (γD), Immunoglobulin E (IgE) or γE-Globulin (γE), Free κ and λ light chains, and Complement factors: C'1, (C'1q, C'1r, C'1s, C'2, C'3 (β 1 A, α 2 D), C'4, C'5, C'6, C'7, C'8, C'9.

[0309] Additional examples of analytes include tumor necrosis factor-α (TNFα), interleukin-12 (IL-12), IL-23, IL-6, α2β1 integrin, α1β1 integrin, α4β7 integrin, integrin α4β1 (VLA-4), E-selectin, ICAM-1, α5β1 integrin, α4β1 integrin, VLA-4, α2β1 integrin, α5β3 integrin, α5β5 integrin, αIIbβ3 integrin, MAdCAM-1, SMAD7, JAK1, JAK2, JAK3, TYK-2, CHST15, IL-1, IL-1α, IL-1ϑ, IL-18, IL-36α, IL-36ϑ, IL-36K, IL-38, IL-33, IL-13, CD40L, CD40, CD3K, CD3δ, CD3ε, CD3ζ, TCR, TCRα, TCRS, TCRδ, TCRK, CD14, CD20, CD25, IL-2, IL-2 ϑ chain, IL-2 K chain, CD28, CD80, CD86, CD49, MMP1, CD89, IgA, CXCL10, CCL11, an ELR chemokine, CCR2, CCR9, CXCR3, CCR3, CCR5, CCL2, CCL8, CCL16, CCL25, CXCR1m CXCR2m CXCL1, CXCL2, CXCL3, CXCL4, CXCL5, CXCL6, CXCL7, and CXCL8, and a nucleic acid (e.g., mRNA) encoding any of the same.

[0310] In some disclosures, the analyte is a blood clotting factor. Exemplary blood clotting factors include, but are not limited to: International designationNameIFibrinogenIIProthrombinIIaThrombinIIITissue thromboplastinV and VIProaccelerin, accelerator globulinVIIProconvertinVIIIAntihemophilic globulin (AHG)IXChristmas factor plasma thromboplastin component (PTC)XStuart-Prower factor, autoprothrombin IIIXIPlasma thromboplastin antecedent (PTA)XIIHagemann factorXIIIFibrin-stabilizing factor

[0311] In some disclosures, the analyte is a hormone. Exemplary hormones include, but are not limited to: Peptide and Protein Hormones, Parathyroid hormone, (parathromone), Thyrocalcitonin, Insulin, Glucagon, Relaxin, Erythropoietin, Melanotropin (melancyte-stimulating hormone; intermedin), Somatotropin (growth hormone), Corticotropin (adrenocorticotropic hormone), Thyrotropin, Follicle-stimulating hormone, Luteinizing hormone (interstitial cell-stimulating hormone), Luteomammotropic hormone (luteotropin, prolactin), Gonadotropin (chorionic gonadotropin), Secretin, Gastrin, Angiotensin I and II, Bradykinin, and Human placental lactogen, thyroxine, cortisol, triiodothyronine, testosterone, estradiol, estrone, progestrone, luteinizing hormone-releasing hormone (LHRH), and immunosuppressants such as cyclosporine, FK506, mycophenolic acid, and so forth.

[0312] In some disclosures, the analyte is a peptide hormone (e.g., a peptide hormone from the neurohypophysis). Exemplary peptide hormones from the neurohypophysis include, but are not limited to: Oxytocin, Vasopressin, and releasing factors (RF) (e.g., corticotropin releasing factor (CRF), luteinizing hormone releasing factor (LRF), thyrotropin releasing factor (TRF), Somatotropin-RF, growth hormone releasing factor (GRF), follicle stimulating hormone-releasing factor (FSH-RF), prolactin inhibiting factor (PIF), and melanocyte stimulating hormone inhibiting factor (MIF)).

[0313] In some disclosures, the analyte is a cytokine or a chemokine. Exemplary cytokines include, but are not limited to: interleukin-1 (IL-1), interleukin-2 (IL-2), interleukin-6 (IL-6), epidermal growth factor (EGF), tumor necrosis factor (TNF, e.g., TNF-α or TNF-β), and nerve growth factor (NGF).

[0314] In some disclosures, the analyte is a cancer antigen. Exemplary cancer antigens include, but are not limited to: prostate-specific antigen (PSA), carcinoembryonic antigen (CEA), α-fetoprotein, Acid phosphatase, CA19.9, CA125, CD19, WT-1, CD22, L1-CAM, ROR-1, CD30, CD125, AFP, CEA, ETA, MAGE, and MUC16.

[0315] In some disclosures, the analyte is a tissue-specific antigen. Exemplary tissue specific antigens include, but are not limited to: alkaline phosphatase, myoglobin, CPK-MB, calcitonin, and myelin basic protein.

[0316] In some disclosures, the analyte is a mucopolysaccharide or a polysaccharide.

[0317] In some disclosures, the analyte is a microorganism, or a molecule derived from or produced by a microorganism (e.g., a bacteria, a virus, prion, or a protozoan). For example, in some disclosures, the analyte is a molecule (e.g., a protein or a nucleic acid) that is specific for a particular microbial genus, species, or strain (e.g., a specific bacterial genus, species, or strain). In some disclosures, the microorganism is pathogenic (i.e., causes disease). In some disclosures, the microorganism is non-pathogenic (e.g., a commensal microorganism). Exemplary microorganisms include, but are not limited to: Corynebacteria Corynebacterium diphtheria Pneumococci Diplococcus pneumoniae Streptococci Streptococcus pyrogenes Streptococcus salivarus Staphylococci Staphylococcus aureus Staphylococcus albus Neisseria Neisseria meningitidis Neisseria gonorrhea Enterobacteriaciae Escherichia coli Aerobacter aerogenes The coliform bacteria Klebsiella pneumoniae Salmonella typhosa Salmonella choleraesuis The Salmonellae Salmonella typhimurium Shigella dysenteria Shigella schmitzii Shigella arabinotarda The Shigellae Shigella flexneri Shigella boydii Shigella sonnei Other enteric bacilli Proteus vulgaris Proteus mirabilis Proteus species Proteus morgani Pseudomonas aeruginosa Alcaligenes faecalis Vibrio cholerae Hemophilus-Bordetella group Rhizopus oryzae Hemophilus influenza, H. ducryi Rhizopus arrhizua Phycomycetes Hemophilus hemophilus Rhizopus nigricans Hemophilus aegypticus Sporotrichum schenkii Hemophilus parainfluenza Flonsecaea pedrosoi Bordetella pertussis Fonsecacea compact Pasteurellae Fonsecacea dermatidis Pasteurella pestis Cladosporium carrionii Pasteurella tulareusis Phialophora verrucosa Brucellae Aspergillus nidulans Brucella melltensis Madurella mycetomi Brucella abortus Madurella grisea Brucella suis Allescheria boydii Aerobic Spore-forming Bacilli Phialophora jeanselmei Bacillus anthracis Microsporum gypseum Bacillus subtilis Trichophyton mentagrophytes Bacillus megaterium Keratinomyces ajelloi Bacillus cereus Microsporum canis Anaerobic Spore-forming Bacilli Trichophyton rubrum Clostridium botulinum Microsporum adouini Clostridium tetani Viruses Clostridium perfringens Adenoviruses Clostridium novyi Herpes Viruses Clostridium septicum Herpes simplex Clostridium histoyticum Varicella (Chicken pox) Clostridium tertium Herpes Zoster (Shingles) Clostridium bifermentans Virus B Clostridium sporogenes Cytomegalovirus Mycobacteria Pox Viruses Mycobacterium tuberculosis hominis Variola (smallpox) Mycobacterium bovis Vaccinia Mycobacterium avium Poxvirus bovis Mycobacterium leprae Paravaccinia Mycobacterium paratuberculosis Molluscum contagiosum Actinomycetes (fungus-ike bacteria) Picornaviruses Actinomyces Isaeli Poliovirus Actinomyces bovis Coxsackievirus Actinomyces naeslundii Echoviruses Nocardia asteroides Rhinoviruses Nocardia brasiliensis Myxoviruses The Spirochetes Influenza(A, B, and C) Treponema pallidum Parainfluenza (1-4) Treponema pertenue Mumps Virus Spirillum minus Streptobacillus monoiliformis Newcastle Disease Virus Treponema carateum Measles Virus Borrelia recurrentis Rinderpest Virus Leptospira icterohemorrhagiae Canine Distemper Virus Leptospira canicola Respiratory Syncytial Virus Trypanasomes Rubella Virus Mycoplasmas Arboviruses Mycoplasma pneumoniae Other pathogens Eastern Equine Encephalitis Virus Listeria monocytogenes Western Equine Encephalitis Virus Erysipeothrix rhusiopathiae Sindbis Virus Streptobacillus moniliformis Chikugunya Virus Donvania granulomatis Semliki Forest Virus Entamoeba histolytica Mayora Virus Plasmodium falciparum St. Louis Encephalitis Plasmodium japonicum California Encephalitis Virus Bartonella bacilliformis Colorado Tick Fever Virus Rickettsia (bacteria-like parasites) Yellow Fever Virus Rickettsia prowazekii Dengue Virus Rickettsia mooseri Reoviruses Rickettsia rickettsii Reovirus Types 1-3 Rickettsia conori Retroviruses Rickettsia australis Human Immunodeficiency Rickettsia sibiricus Viruses I and II (HTLV) Rickettsia akari Human T-cell Lymphotrophic Rickettsia tsutsugamushi Virus I & II (HIV) Rickettsia burnetti Hepatitis Rickettsia quintana Hepatitis A Virus Chlamydia (unclassifiable parasites bacterial / viral) Hepatitis B Virus Hepatitis C Virus Chlamydia agents (naming uncertain) Tumor Viruses Chlamydia trachomatis Fungi Rauscher Leukemia Virus Cryptococcus neoformans Gross Virus Blastomyces dermatidis Maloney Leukemia Virus Histoplasma capsulatum Coccidioides immitis Human Papilloma Virus Paracoccidioides brasliensis Candida albicans Aspergillus fumigatus Mucor corymbifer (Absidia corymbifera)

[0318] In some disclosures, the analyte is a bacterium. Exemplary bacteria include, but are not limited to: Escherichia coli (or E. coli), Bacillus anthracis, Bacillus cereus, Clostridium botulinum, Clostridium difficile, Yersinia pestis, Yersinia enterocolitica, Francisella tularensis, Brucella species, Clostridium perfringens, Burkholderia mallei, Burkholderia pseudomallei, Staphylococcus species, Mycobacterium species, Group A Streptococcus, Group B Streptococcus, Streptococcus pneumoniae, Helicobacter pylori, Salmonella enteritidis, Mycoplasma hominis, Mycoplasma orale, Mycoplasma salivarium, Mycoplasma fermentans, Mycoplasma pneumoniae, Mycobacterium bovis, Mycobacterium tuberculosis, Mycobacterium avium, Mycobacterium leprae, Rickettsia rickettsii, Rickettsia akari, Rickettsia prowazekii, Rickettsia canada, Bacillus subtilis, Bacillus subtilis niger, Bacillus thuringiensis, Coxiella burnetti, Faecalibacterium prausnitzii (also known as Bacteroides praussnitzii), Roseburia hominis, Eubacterium rectale, Dialister invisus, Ruminococcus albus, Ruminococcus callidus, and Ruminococcus bromii. Additional exemplary bacteria include bacteria of the phyla Firmicutes (e.g., Clostridium clusters XIVa and IV), bacteria of the phyla Bacteroidetes (e.g., Bacteroides fragilis or Bacteroides vulgatus), and bacteria of the phyla Actinobacteria (e.g., Coriobacteriaceae spp. or Bifidobacterium adolescentis). Bacteria of the Clostridium cluster XIVa includes species belonging to, for example, the Clostridium, Ruminococcus, Lachnospira, Roseburia, Eubacterium, Coprococcus, Dorea, and Butyrivibrio genera. Bacteria of the Clostridium cluster IV includes species belonging to, for example, the Clostridium, Ruminococcus, Eubacterium and Anaerofilum genera. In some disclosures, the analyte is Candida, e.g., Candida albicans. In some disclosures, the analyte is a byproduct from a bacterium or other microorganism, e.g., helminth ova, enterotoxin (Clostridium difficile toxin A; TcdA) or cytotoxin (Clostridium difficile toxin B; TcdB).

[0319] In some disclosures, the analyte is a pathogenic bacterium. Non-limiting examples of pathogenic bacteria belong to the genera Bacillus, Bordetella, Borrelia, Brucella, Campylobacter, Chlamydia, Chlamydophila, Clostridium, Corynebacterium, Enterobacter, Enterococcus, Escherichia, Francisella, Haemophilus, Helicobacter, Legionella, Leptospira, Listeria, Mycobacterium, Mycoplasma, Neisseria, Pseudomonas, Rickettsia, Salmonella, Shigella, Staphylococcus, Streptococcus, Treponema, Vibrio, and Yersinia. Non-limiting examples of specific pathogenic bacterial species include a strain of Bacillus anthracis, a strain of a strain of Bordetella pertussis, a strain of a strain of Borrelia burgdorferi, a strain of a strain of Brucella abortus, a strain of a strain of Brucella canis, a strain of a strain of Brucella melitensis, a strain of a strain of Brucella suis, a strain of a strain of Campylobacter jejuni, a strain of Chlamydia pneumoniae, a strain of Chlamydia trachomatis, a strain of Chlamydophila psittaci, a strain of Clostridium botulinum, a strain of Clostridium difficile, a strain of Clostridium perfringens, a strain of Clostridium tetani, a strain of Corynebacterium diphtheria, a strain of Enterobacter sakazakii, a strain of Enterococcus faecalis, a strain of Enterococcus faecium, a strain of Escherichia coli (e.g., E. coli 0157 H7), a strain of Francisella tularensis, a strain of Haemophilus influenza, a strain of Helicobacter pylori, a strain of Legionella pneumophila, a strain of Leptospira interrogans, a strain of Listeria monocytogenes, a strain of Mycobacterium leprae, a strain of Mycobacterium tuberculosis, a strain of Mycobacterium ulcerans, a strain of Mycoplasma pneumonia, a strain of Neisseria gonorrhoeae, a strain of Neisseria meningitides, a strain of Pseudomonas aeruginosa, a strain of Rickettsia rickettsia, a strain of Salmonella typhi and Salmonella typhimurium, a strain of Shigella sonnei, a strain of Staphylococcus aureus, a strain of Staphylococcus epidermidis, a strain of Staphylococcus saprophyticus, a strain of Streptococcus agalactiae, a strain of Streptococcus pneumonia, a strain of Streptococcus pyogenes, a strain of Treponema pallidum, a strain of Vibrio cholera, a strain of Yersinia enterocolitica, and, a strain of Yersinia pestis.

[0320] In some disclosures, the analyte is a commensal bacterium (e.g., a probiotic). In some disclosures, the bacterium has been previously administered to a subject, e.g., as a live biotherapeutic agent. Exemplary commensal bacteria include, but are not limited to, Faecalibacterium prausnitzii (also referred to as Bacteroides praussnitzii), Roseburia hominis, Eubacterium rectale, Dialister invisus, Ruminococcus albus, Ruminococcus gnavus, Ruminococcus torques, Ruminococcus callidus, and Ruminococcus bromii.

[0321] In some disclosures, the analyte is a virus. In some disclosures, the virus is a pathogenic virus. Non-limiting examples of pathogenic viruses belong to the families Adenoviridae, Picornaviridae, Herpesviridae, Hepadnaviridae, Flaviviridae, Retroviridae, Orthomyxoviridae, Paramyxoviridae, Papovaviridae, Polyomavirus, Rhabdoviridae, and Togaviridae. In some disclosures, the analyte is a bacteriophage. In some disclosures, the devices and methods described herein are used to identify, characterize and / or quantify the virome in the GI tract of a subject (e.g., in vivo or ex vivo). In some disclosures, the relative abundance of Escherichia phage, Enterobacteria phage, and Caudovirales bacteriophages is determined using the devices and methods described herein, wherein Escherichia phage and Enterobacteria phage are more abundant in the mucosa of IBD patients than healthy controls.

[0322] In some disclosures, the analyte is a fungus. In some disclosures, the fungi is a pathogenic fungus. Non-limiting examples of pathogenic fungi belong to the genera Asperfillus, Canidia, Cryptococcus, Histoplasma, Pneumocystis, and Stachybotrys. Non-limiting examples of specific pathogenic fungi species include a strain of Aspergillus clavatus, Aspergillus fumigatus, Aspergillus flavus, Canidia albicans, Cryptococcus albidus, Cryptococcus gattii, Cryptococcus laurentii, Cryptococcus neoformans, Histoplasma capsulatum, Pneumocystis jirovecii, Pneumocystis carinii, and Stachybotrys chartarum.

[0323] In some disclosures, the analyte is a protozoan. In some disclosures, the analyte is a pathogenic protozoan. Non-limiting examples of pathogenic protozoa belong to the genera Acanthamoeba, Balamuthia, Cryptosporidium, Dientamoeba, Endolimax, Entamoeba, Giardia, Iodamoeba, Leishmania, Naegleria, Plasmodium, Sappinia, Toxoplasma, Trichomonas, and Trypanosoma. Non-limiting examples of specific pathogenic protozoa species include a strain of Acanthamoeba spp., Balamuthia mandrillaris, Cryptosporidium canis, Cryptosporidium felis, Cryptosporidium hominis, Cryptosporidium meleagridis, Cryptosporidium muris, Cryptosporidium parvum, Dientamoeba fragilis, Endolimax nana, Entamoeba dispar, Entamoeba hartmanni, Entamoeba histolytica, Entamoeba coli, Entamoeba moshkovskii, Giardia lamblia, Iodamoeba butschlii, Leishmania aethiopica, Leishmania braziliensis, Leishmania chagasi, Leishmania donovani, Leishmania infantum, Leishmania major, Leishmania mexicana, Leishmania tropica, Naegleria fowleri, Plasmodium falciparum, Plasmodium knowlesi, Plasmodium malariae, Plasmodium ovale, Plasmodium vivax, Sappinia diploidea, Toxoplasma gondii, Trichomonas vaginalis, Trypanosoma brucei, and Trypanosoma cruzi.

[0324] In some disclosures, the analyte is secreted by or expressed on the cell surface of a microorganism (e.g., a bacterium, a colonic bacterium, a viable bacterium, a dead bacterium, a parasite (e.g., Giardia lamblia, Cryptosporidium, Cystoisosporiasis belli, and Balantidium coli), a virus (e.g., a herpes virus, a cytomegalovirus, a herpes simplex virus, an Epstein-Barr virus, a human papilloma virus, a rotavirus, a human herpesvirus-8; Goodgame (1999) Curr. Gastroenterol. Rep. 1(4):292-300). In some disclosures, the analyte is secreted by or expressed on the cell surface of a Gram-negative bacterium (e.g., E. coli, Helicobacter pylori). In some disclosures, the analyte is secreted by or expressed on the cell surface (e.g., a bacterial surface epitope) of a Gram-positive bacterium (e.g., Staphylococcus aureus, Clostridium botulinum, Clostridium difficile).

[0325] In some disclosures, the analyte is a molecule expressed on the surface of a bacterial cell (e.g., a bacterial cell surface protein). In some disclosures, the analyte is a bacterial toxin (e.g., TcdA and / or TcdB from Clostridium difficile). In some disclosures, the analyte is CFA / I fimbriae, flagella, lipopolysaccharide (LPS), lipoteichoic acid, or a peptidoglycan. Non-limiting examples of bacterium that may express an analyte that can be detected using any of the devices and methods described herein include: Bacillus anthracis, Bacillus cereus, Clostridium botulinum, Clostridium difficile, Escherichia coli, Yersinia pestis, Yersinia enterocolitica, Francisella tularensis, Brucella species, Clostridium perfringens, Burkholderia mallei, Burkholderia pseudomallei, Helicobacter pylori, Staphylococcus species, Mycobacterium species, Group A Streptococcus, Group B Streptococcus, Streptococcus pneumoniae, Francisella tularensis, Salmonella enteritidis, Mycoplasma hominis, Mycoplasma orale, Mycoplasma salivarium, Mycoplasma fermentans, Mycoplasma pneumoniae, Mycobacterium bovis, Mycobacterium tuberculosis, Mycobacterium avium, Mycobacterium leprae, Rickettsia rickettsii, Rickettsia akari, Rickettsia prowazekii, Rickettsia canada, Bacillus subtilis, Bacillus subtilis niger, Bacillus thuringiensis, Coxiella bumetti, Candida albicans, Bacteroides fragilis, Leptospira interrogans, Listeria monocytogenes, Pasteurella multocida, Salmonella typhi, Salmonella typhimurium, Shigella dysenteriae, Shigella flexneria, Shigella sonnei, Vibrio cholera, and Vibrio parahaemolyticus.

[0326] In some disclosures, the analyte is a byproduct from a bacterium or another microorganism, e.g., helminth ova, enterotoxin (Clostridium difficile toxin A; TcdA), cytotoxin (Clostridium difficile toxin B; TcdB), and ammonia. In some disclosures, the analyte is an antigen from a microorganism (e.g., a bacteria, virus, prion, fungus, protozoan or a parasite).

[0327] In some disclosures, the analytes include drugs, metabolites, pesticides, pollutants, and the like. Included among drugs of interest are the alkaloids. Among the alkaloids are morphine alkaloids, which includes morphine, codeine, heroin, dextromethorphan, their derivatives and metabolites; cocaine alkaloids, which include cocaine and benzyl ecgonine, their derivatives and metabolites; ergot alkaloids, which include the diethylamide of lysergic acid; steroid alkaloids; iminazoyl alkaloids; quinazoline alkaloids; isoquinoline alkaloids; quinoline alkaloids, which include quinine and quinidine; diterpene alkaloids, their derivatives and metabolites.

[0328] In some disclosures, the analyte is a steroid selected from the estrogens, androgens, adrenocortical steroids, bile acids, cardiotonic glycosides and aglycones, which includes digoxin and digoxigenin, saponins and sapogenins, their derivatives and metabolites. Also included are the steroid mimetic substances, such as diethylstilbestrol.

[0329] In some disclosures, the analyte is a bile acid or a bile salt (also known as a conjugated bile acid). Bile acids are products of cholesterol synthesis that are synthesized in the liver, conjugated to taurine or glycine, and stored in the gallbladder until released into the small intestine. The primary bile acids are cholic acid, and chenodeoxycholic acid, which are deconjugated and dehydroxylated by intestinal bacteria (bile acid (BA)-metabolizing microbiota (BAMM)) to form the secondary bile acids deoxycholic acid and lithocholic acid, respectively. BA-metabolizing microbiota (BAMM) have been shown to influence host homeostasis through changes in BA composition. The devices and methods described herein may be used to identify, characterize and / or quantify BAMM in the GI tract of a subject (e.g., in vivo or ex vivo), for example, using the Clusters of Orthologous Groups (COG) database, which provides the distribution of bacterial functions in the core and dispensable genomes (Tatusov, R. L. et al., "The COG database: an updated version includes eukaryotes," BMC Bioinformatics 4:41 (2003)). In some disclosures, higher abundance of BAMM associated with bile salt hydrolase (BSH) activity (e.g., COG3049) is associated with IBD, higher abundance of BAMM associated with hydroxysteroid dehydrogenase (HSDH) activity (e.g., COG1902) is associated with Crohn's disease, and higher abundance of BAMM associated with alphadehydoxylase (ADH) activity (e.g., COG1062) is associated with inflamed GI mucosa, wherein abundance is relative to levels seen in healthy controls. The majority of bile acids (about 95%) are reabsorbed in the distal ileum and returned to the liver (see, e.g., U.S. Publication No. 2017 / 0343535). Impaired absorption of bile acids in the ileum can lead to excess bile acids in the colon which can cause symptoms of bile acid malabsorption (BAM; also known as bile acid diarrhea), including watery stool and fecal incontinence. Interestingly, up to 50% of patients with irritable bowel syndrome with diarrhea (IBS-D) also have BAM (see, e.g., Camilleri et al. (2009) Neurogastroeterol. Motil. 21(7):734-43). In some disclosures, the presence, absence, and / or a specific level of one or more bile acids or bile salts in the GI tract of a subject is indicative of a condition or disease state (e.g., a GI disorder and / or a non-GI disorder (e.g., a systemic disorder or a liver disease)). In some disclosures, the compositions, devices, and methods described herein may be used to detect, analyze and / or quantify at least one bile acid or bile salt in the GI tract of the subject to diagnose a GI disorder such as BAM or IBS (e.g., IBS-D). In some disclosures, the devices, methods and compositions described herein can be used to detect, quantitate, and / or analyze a bile acid or a bile salt in the GI tract of a subject. For instance, the presence and / or absence, and / or the concentration of a bile acid, a bile salt, or a combination thereof, may be determined at a specific region of the GI tract of a subject (e.g., one or more of the duodenum, jejunum, ileum, ascending colon, transverse colon or descending colon) to determine whether the subject has or is at risk of developing a GI disorder, such as BAM or IBS-D. In some disclosures, the devices, methods and compositions described herein can be used to determine the ratio of two or more bile acids or bile acid salts in the GI tract of a subject (e.g., a specific region of the GI tract of a subject including one or more of the duodenum, jejunum, ileum, ascending colon, transverse colon or descending colon). In some disclosures, the presence and / or absence, and / or the concentration of a bile acid, a bile salt, or a combination thereof, is determined in the ileum of a subject. In some disclosures, the presence and / or absence, and / or the concentration of a bile acid, a bile salt, or a combination thereof, is determined in the colon of a subject. In some disclosures, the concentration of a bile acid, a bile salt, or a combination thereof, is determined in specific regions of the GI tract of the subject, and for example, compared to determine where along the GI tract the compounds are accumulating. In some disclosures, the detection of a concentration of a bile acid, bile salt, or a combination thereof, in a specific region of the GI tract of the subject (e.g., the colon or the ileum) that is above a reference level of a bile acid, bile salt, or a combination thereof (e.g., the average level of a bile acid in healthy subjects) may be indicative of BAM and / or IBS-D in a subject. In some disclosures, the bile acid is selected from the group consisting of chenodeoxycholic acid, cholic acid, deoxycholate, lithocholate, and ursodeoxycholic acid. In some disclosures, the bile acid comprises cholesten-3-one or a structural variant thereof. In some disclosures, the bile acid is cholesten-3-one or a structural variant thereof. In some disclosures, the bile acid is cholesten-3-one. In some disclosures, the bile acid is a structural variant of cholesten-3-one. In some embodiments, the bile salt is selected from the group consisting of glycocholic acid, taurocholic acid, glycodeoxycholic acid, glycochenodeoxycholic acid, taurodeoxycholic acid, taurochenodeoxycholic acid, glycolithocholic acid, and taurolithocholic acid.

[0330] In some disclosures, the analyte is 7α-hydroxy-4-cholesten-3-one (7αC4). The measurement of 7αC4 allows for the monitoring of the enzymatic activity of hepatic cholesterol 7α-hydroxylase, the rate limiting enzyme in the synthesis of bile acids and can be used as a surrogate to detect BAM (see, e.g., Galman et al. (2003) J. Lipid. Res. 44:859-66; and Camilleri et al. (2009) Neurogastroeterol. Motil. 21(7):734-43).

[0331] In some disclosures, the analyte comprises cholesterol, a lipid, a fat soluble vitamin (e.g., ascorbic acid, cholecalciferol, ergocalciferol, a tocopherol, a tocotrienol, phylloquinone, and a menaquinone), bilirubin, fibroblast growth factor 19 (FGF19), TGR5 (also known as GP-BAR1 or M-BAR), glycine, taurine, or cholecystokinin (CCK or CCK-PZ). In some disclosures, the analyte comprises cholecystokinin. Cholecystokinin is a peptide hormone that contributes to control intestinal motility (see Rehfeld (2017) Front. Endocrinol. (Lausanne) 8:47). In some disclosures, the analyte comprises secretin. Secretin is a peptide hormone that regulates the pH of the duodenal content by controlling gastric acid secretion, regulates bile acid and bicarbonate secretion in the duodenum, and regulates water homeostasis (see, e.g., Afroze et al. (2013) Ann. Transl. Med. 1(3):29). In some disclosures, a subject has been administered cholecystokinin or secretin to induce the release of an analyte (e.g., from the liver and / or gall bladder into the GI tract).

[0332] In some disclosures, the analyte is a metabolite in the serotonin, tryptophan and / or kynurenine pathways, including but not limited to, serotonin (5-HT), 5-hydroxyindole acetic acid (5-HIAA), 5-hydroxytryptophan (5-HTP), kynurenine (K), kynurenic acid (KA), 3-hydroxykynurenine (3-HK), 3-hydroxyanthranilic acid (3-HAA), quinolinic acid, anthranilic acid, and combinations thereof. 5-HT is a molecule that plays a role in the regulation of gastrointestinal motility, secretion, and sensation. Imbalances in the levels of 5-HT are associated with several diseases including inflammatory bowel syndrome (IBS), autism, gastric ulcer formation, non-cardiac chest pain, and functional dyspepsia (see, e.g., Faure et al. (2010) Gastroenterology 139(1):249-58 and Muller et al. (2016) Neuroscience 321:24-41, and International Publication No. WO 2014 / 188377). Conversion of metabolites within the serotonin, tryptophan and / or kynurenine pathways affects the levels of 5-HT in a subject. Therefore, measuring the levels of one or more of the metabolites in this pathway may be used for the diagnosis, management and treatment of a disease or disorder associated with 5-HT imbalance including but not limited to IBS, autism, carcinoid syndrome, depression, hypertension, Alzheimer's disease, constipation, migraine, and serotonin syndrome. One or more analytes in the serotonin, tryptophan and / or kynurenine pathways can be detected and / or quantitated using, for example, methods and analyte-binding agents that bind to these metabolites including, e.g., antibodies, known in the art (see, e.g., International Publication No. WO 2014 / 188377).

[0333] In some disclosures, the analyte is a lactam having from 5 to 6 annular members selected from barbiturates, e.g., phenobarbital and secobarbital, diphenylhydantoin, primidone, ethosuximide, and metabolites thereof.

[0334] In some disclosures, the analyte is an aminoalkylbenzene, with alkyl of from 2 to 3 carbon atoms, selected from the amphetamines; catecholamines, which includes ephedrine, L-dopa, epinephrine; narceine; papaverine; and metabolites thereof.

[0335] In some disclosures, the analyte is a benzheterocyclic selected from oxazepam, chlorpromazine, tegretol, their derivatives and metabolites, the heterocyclic rings being azepines, diazepines and phenothiazines.

[0336] In some disclosures, the analyte is a purine selected from theophylline, caffeine, their metabolites and derivatives.

[0337] In some disclosures, the analyte is marijuana, cannabinol or tetrahydrocannabinol.

[0338] In some disclosures, the analyte is a vitamin such as vitamin A, vitamin B, e.g. vitamin B 12 , vitamin C, vitamin D, vitamin E and vitamin K, folic acid, thiamine.

[0339] In some disclosures, the analyte is selected from prostaglandins, which differ by the degree and sites of hydroxylation and unsaturation.

[0340] In some disclosures, the analyte is a tricyclic antidepressant selected from imipramine, dismethylimipramine, amitriptyline, nortriptyline, protriptyline, trimipramine, chlomipramine, doxepine, and desmethyldoxepin.

[0341] In some disclosures, the analyte is selected from anti-neoplastics, including methotrexate.

[0342] In some disclosures, the analyte is an antibiotic as described herein, including, but not limited to, penicillin, chloromycetin, actinomycetin, tetracycline, terramycin, and metabolites and derivatives.

[0343] In some disclosures, the analyte is a nucleoside or nucleotide selected from ATP, NAD, FMN, adenosine, guanosine, thymidine, and cytidine with their appropriate sugar and phosphate substituents.

[0344] In some disclosures, the analyte is selected from methadone, meprobamate, serotonin, meperidine, lidocaine, procainamide, acetylprocainamide, propranolol, griseofulvin, valproic acid, butyrophenones, antihistamines, chloramphenicol, anticholinergic drugs, such as atropine, their metabolites and derivatives.

[0345] In some disclosures, the analyte is a metabolite related to a diseased state. Such metabolites include, but are not limited to spermine, galactose, phenylpyruvic acid, and porphyrin Type 1.

[0346] In some disclosures, the analyte is an aminoglycoside, such as gentamicin, kanamicin, tobramycin, or amikacin.

[0347] In some disclosures, the analyte is a pesticide. Among pesticides of interest are polyhalogenated biphenyls, phosphate esters, thiophosphates, carbamates, polyhalogenated sulfenamides, their metabolites and derivatives.

[0348] In some disclosures, the analyte has a molecular weight of about 500 Da to about 1,000,000 Da (e.g., about 500 to about 500,000 Da, about 1,000 to about 100,000 Da).

[0349] In some disclosures, the analyte is a receptor, with a molecular weight ranging from about 10,000 to about 2 x 10 8< Da, more usually from about 10,000 to about 10 6< Da. For immunoglobulins, IgA, IgG, IgE and IgM, the molecular weights will generally vary from about 160,000 Da to about 10 6< Da. Enzymes will normally range in molecular weight from about 10,000 Da to about 1,000,000 Da. Natural receptors vary widely, generally having a molecular weight of at least about 25,000 Da and may be about 10 6< or higher Da, including such materials as avidin, DNA, RNA, thyroxine binding globulin, thyroxine binding prealbumin, transcortin, etc.

[0350] In some disclosures, the term "analyte" further includes polynucleotide analytes such as those polynucleotides defined below. These include m-RNA, r-RNA, t-RNA, DNA, DNA-DNA duplexes, DNA-RNA duplexes, nucleic acid molecules comprising modified bases, locked nucleic acid molecules (LNA molecules), antagomirs, peptide nucleic acid molecules (PNA molecules), antisense RNA or DNA molecules (e.g., antisense molecules including modifications to the sugars, bases, backbone linkages that allow for specific detection), chimeric antisense oligonucleotides, antisense oligonucleotides comprising modified linkages, interference RNA (RNAi), short interfering RNA (siRNA); a micro, interfering RNA (miRNA); a small, temporal RNA (stRNA); or a short, hairpin RNA (shRNA); small RNA-induced gene activation (RNAa); small activating RNAs (saRNAs), etc. The term analyte also includes polynucleotide-binding agents, such as, for example, restriction enzymes, transcription factors, transcription activators, transcription repressors, nucleases, polymerases, histones, DNA repair enzymes, intercalating agents, chemotherapeutic agents, and the like.

[0351] In some disclosures, the analyte may be a molecule found directly in a sample such as a body fluid from a host. The sample can be examined directly or may be pretreated to render the analyte more readily detectible. Furthermore, the analyte of interest may be determined by detecting an agent probative of the analyte of interest (e.g., an analyte-binding agent), such as a specific binding pair member complementary to the analyte of interest, whose presence will be detected only when the analyte of interest is present in a sample. Thus, the agent probative of the analyte becomes the analyte that is detected in an assay.

[0352] In some disclosures, the analyte a nucleic acid (e.g., a bacterial DNA molecule or a bacterial RNA molecule (e.g., a bacterial tRNA, a transfer-messenger RNA (tmRNA)). See, e.g., Sjostrom et al. (2015) Scientific Reports 5:15329; Ghosal (2017) Microbial Pathogenesis 104:161-163; Shen et al. (2012) Cell Host Microbe. 12(4):509-520.

[0353] In some disclosures, the analyte is a component of an outer membrane vesicle (OMV) (e.g., an OmpU protein, Elluri et al. (2014) PloS One 9:e106731). See, e.g., Kulp and Kuehn (2010) Annual Review of microbiology 64:163-184; Berleman and Auer (2013) Environmental microbiology 15:347-354; Wai et al. (1995) Microbiology and immunology 39:451-456; Lindmark et al. (2009) BMC Microbiology 9:220; Sjostrom et al. (2015) Scientific Reports 5:15329.

[0354] In some disclosures, the analyte is G-CSF, which can stimulate the bone marrow to produce granulocytes and stem cells and release them into the bloodstream.

[0355] In some disclosures, the analyte is an enzyme such as glutathione S-transferase. For example, the ingestible device can include P28GST, a 28 kDa helminth protein from Schistosoma with potent immunogenic and antioxidant properties. P28GST prevents intestinal inflammation in experimental colitis through a Th2-type response with mucosal eosinophils and can be recombinantly produced (e.g., in S. cerevisiae). See, for example, U.S. Patent No. 9,593,313, Driss et al., Mucosal Immunology, 2016 9, 322-335; and Capron et al., Gastroenterology, 146(5):S-638.

[0356] In some disclosures, the analyte is a metabolite in the serotonin, tryptophan and / or kynurenine pathways, including but not limited to, serotonin (5-HT), 5-hydroxyindole acetic acid (5-HIAA), 5-hydroxytryptophan (5-HTP), kynurenine (K), kynurenic acid (KA), 3-hydroxykynurenine (3-HK), 3-hydroxyanthranilic acid (3-HAA), quinolinic acid, anthranilic acid, and combinations thereof.

[0357] In some disclosures, analytes are therapeutic agents, fragments thereof, and metabolites thereof (e.g., antibiotics). In some disclosures, analytes are biomarkers. In some disclosures, the analytes are antibodies. In some disclosures, the analytes are antibiotics. Exemplary antibiotic agents are set forth in the U.S. Patent Publication US 2006 / 0269485. Additional exemplary analytes (e.g., therapeutic agents (e.g., drugs), antibodies, antibiotics and biomarkers) are provided below. Additional exemplary analytes (e.g., biomarkers, antibodies, antibiotics, and therapeutic agents) are described in International Publication No. PCT / US2017 / 065139, filed December 7, 2017.Analyte-Binding Agents

[0358] Certain detection methods described below can utilize at least one analyte-binding agent in order to detect an analyte in a sample. An "analyte-binding agent" is a molecule that binds to a specific analyte. Some analyte-binding agents may comprise analytes (e.g., the analytes described above) in accordance with the ability of the analyte to bind to another molecule to be detected using the methods described below. For example, in some disclosures, the analyte-binding agent comprises an antibody when used as a reagent to detect and / or quantify an antigen that the antibody specifically binds to. However, in some disclosures, the antibody is an analyte (e.g., an antibody which is a drug, such as a TNFα antibody) and the analyte-binding agent comprises an antigen to which the antibody specifically binds, thereby allowing for its use as a reagent to detect and / or quantify the antibody. In some disclosures, the analyte-binding agent binds to analyte that is specific to a particular genus, species, or strain of a microorganism (e.g., a pathogenic bacteria). In some embodiments, an analyte-binding agent has an area on the surface or in a cavity which specifically binds to and is thereby defined as complementary with a particular spatial and polar organization of the analyte. In some disclosures, the analyte-binding agent and the corresponding analyte form a binding pair, such as, but not limited to, an immunological pair (such as antigen-antibody), a biotin-avidin pair, a hormone-hormone receptor pair, a nucleic acid duplex, IgG-protein A pair, a polynucleotide pair such as DNA-DNA, DNA-RNA, and the like. In some embodiments, the analyte-binding agent comprises an antibody (e.g., a monoclonal antibody), an affimer, an aptamer, an antigen, a receptor, a small molecule, and a nucleic acid (e.g., a DNA molecule or an RNA molecule). In some disclosures, either member of the binding pair (e.g., the analyte-binding agent and / or the analyte) can be detectably labeled as described herein.

[0359] In some disclosures, the analyte-binding agent comprises a portion of a nucleic acid that is complementary to the nucleic acid sequence of the target analyte. As used herein, "complementary" refers to the capacity for pairing through hydrogen binding between two nucleic acid sequences. For example, if a nucleic acid base at one position of the target analyte is capable of hydrogen bonding with a nucleic acid base at a corresponding position of an analyte-binding agent, then the bases are considered to be complementary to each other at that position. In some disclosures, 100% complementarity is not required. In some disclosures, 100% complementarity is required. Routine methods can be used to design an analyte-binding agent that binds to a nucleic acid sequence of a target analyte. In some disclosures, the analyte-binding agent comprises a nucleic acid sequence that is complementary to at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65 or more contiguous nucleotides or nucleosides present in the nucleic acid sequence of the target analyte (e.g., a DNA molecule or an RNA molecule). In general, the analyte-binding agents useful in the devices and methods described herein have at least about 80% sequence complementarity to a nucleic acid sequence of a target analyte, e.g., at least about 85%, at least about 90%, at least about 92%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or are about 100% complementary to a nucleic acid sequence of a target analyte).

[0360] In some disclosures, the analyte-binding agent comprises a detectable moiety such as a photosensitizer, a fluorescent compound, and / or chemiluminescent compound described herein. In some disclosures, the analyte-binding agent is capable of being detected by a detection system of a device described herein, e.g., an optical detection system.Ingestible Devices

[0361] Ingestible devices and their use are described, for example, in the following U.S. patent applications: USSN 14 / 460,893, entitled "Ingestible Medical Device," and filed August 15, 2014; USSN 15 / 514,413, entitled "Electromechanical Pill Device with Localization Capabilities," and filed March 24, 2017; USSN 15 / 680,400, entitled "Systems and Methods for Obtaining Samples using Ingestible Devices," filed on August 18, 2017; USSN 15 / 680,430, entitled "Sampling Systems and Related Materials and Methods," filed on August 18, 2017; USSN 15 / 699,848, entitled "Electromechanical Ingestible Delivery of a Dispensable Substance," filed on September 8, 2017; USSN 15 / 835,270, entitled "Gastrointestinal Tract Detection Methods, Device and Systems," and filed December 7, 2017; USSN 15 / 835,237, entitled "Gastrointestinal Tract Detection Methods, Device and Systems," and filed December 7, 2017; USSN 15 / 835,292, entitled "Gastrointestinal Tract Detection Methods, Device and Systems," and filed December 7, 2017; USSN 15 / 844,349, entitled "Ingestible Device and Associated Methods," filed December 15, 2017; USSN 15 / 844,381, entitled "Ingestible Device and Associated Methods," filed December 15, 2017; USSN 15 / 844,427, entitled "Ingestible Device and Associated Methods," filed December 15, 2017; 15 / 694,458, entitled "Systems and Methods for Extracting a Sample from an Ingestible Device," filed on March 15, 2018; USSN 15 / 940,407, entitled "Localization Systems and Methods for an Optoelectromechanical Pill Device," filed on March 29, 2018; and and USSN 62 / 642,544, entitled "Ingestible Device With Relatively Large Payload Volume," and filed March 13, 2018.

[0362] In general, an ingestible device is configured to be able to enter the GI tract (e.g., via the mouth) and collect one or more samples while passing through one or more regions of the GI tract. Optionally, the device can include one or more additional functionalities, including the ability to analyze the sample while in the GI tract of the subject (in vivo), the ability to deliver a substance (e.g., a therapeutic agent) while in the GI tract of the subject (in vivo) and / or the ability to locate the device outside the GI tract of the subject (ex vivo).

[0363] The ingestible device described herein may generally be in the shape of a capsule, like a conventional pill. As described herein, the device is an ingestible device. Accordingly, the shape of the device provides for easier ingestion, or insertion and removal, and is also familiar to healthcare practitioners and patients.

[0364] Unlike a conventional pill, the device is designed to withstand the chemical and mechanical environment of the GI tract (e.g., effects of muscle contractile forces and concentrated hydrochloric acid in the stomach). However, unlike other devices that are intended to stay inside a patient's body (e.g., medical implants), the ingestible device is designed (in general) to only temporarily travel within the body. Accordingly, the regulatory rules governing the materials and manufacture of the ingestible device may be less strict than for the devices that are intended to stay inside the body. Nevertheless, since the ingestible device still enters the body, the material(s) used to manufacture the ingestible device are generally selected to at least comply with the standards for biocompatibility (e.g., ISO 10993). Furthermore, components inside the ingestible device are free of any restricted and / or toxic metals and are lead-free pursuant to the Directive 2002 / 95 / EC, which is also known as the Restriction of Hazardous Substances (RoHS).

[0365] There is a broad range of materials that may be used for manufacturing the ingestible device. Different materials may be used for each of the different components of the ingestible device. Examples of these materials include, but are not limited to, thermoplastics, fluoropolymers, elastomers, stainless steel and glass complying with ISO 10993 and USP Class VI specifications for biocompatibility. In certain embodiments, these materials may further include liquid silicone rubber material with a hardness level of 10 to 90 as determined using a durometer (e.g., MED-4942 ™< manufactured by NuSil ™< ), a soft biocompatible polymer material such as, but not limited to, polyvinyl chloride (PVC), polyethersulfone (PES), polyethylene (PE), polyurethane (PU) or polytetrafluoroethylene (PTFE), and a rigid polymer material coated with a biocompatible material that is soft or pliable (e.g., a poly(methyl methacrylate) (PMMA) material coated with silicone polymer). Use of different materials for different components may enable functionalization of certain surfaces for interaction with proteins, antibodies, and other biomarkers. For example, Teflon ®< may be used as a material in the ingestible device for any movable components in order to reduce friction between these components. Other example materials may include other materials commonly used in microfabrication, such as polydimethylsiloxane (PDMS), borosilicate glass, and / or silicon.

[0366] Generally, an enclosure of the ingestible device may be manufactured from a type of plastic, such as a photosensitive acrylic polymer material. The enclosure may be formed by coupling two enclosure ends together. The enclosure, in effect, protects the interior of the ingestible device from its external environment and also protects the external environment (e.g., the GI tract) from components inside the device.

[0367] Furthermore, the device may include one or more additional layers of protection. The additional protection may protect the patient against any adverse effects arising from any structural problems associated with the enclosure (e.g., the two enclosure ends falling apart or a fracture developing in the enclosure). For example, a power supply inside the device may be coated with an inert and pliable material (e.g., a thin layer of silicone polymer) so that only electrical contacts on the power supply are exposed. This additional protection to the power supply may prevent chemicals inside the device from seeping into the patient's body.

[0368] Also, a surface of the device and surfaces of the different components in the device may receive different treatments that vary according to their intended use. For example, the surface of the device may receive plasma activation for increasing hydrophilic behavior. Dilution chambers, storage components, ports, valves, pumps and / or conduits that are intended to come into contact with a fluid such as biological fluid or dilution fluid during normal operation of the device may also receive hydrophilic treatment while certain other components may receive hydrophobic treatments.

[0369] FIG. 1 illustrates an example ingestible device 100 with multiple openings in the housing. The ingestible device 100 has an outer housing with a first end 102A, a second end 102B, and a wall 104 extending longitudinally from the first end 102A to the second end 102B. Ingestible device 100 has a first opening 106 in the housing, which is connected to a second opening 108 in the housing. The first opening 106 of the ingestible device 100 is oriented substantially perpendicular to the second opening 108, and the connection between the first opening 106 and the second opening 108 forms a curved chamber 110 within the ingestible device 100.

[0370] The overall shape of the ingestible device 100, or any of the other ingestible devices discussed in this disclosure, may be similar to an elongated pill or capsule. This may make the ingestible device 100 easy to consume, and allow it to travel easily through the GI tract. In certain portions of the GI tract, such as the stomach, the ingestible device 100 may be free to move or rotate in any direction. In other portions of the GI tract, the movement of the ingestible device 100 may be restricted. For example, in the relatively narrow confines of the small intestine, the walls of the small intestine may squeeze down on the ingestible device, forcing the ingestible device 100 to orient itself longitudinally along the length of the small intestine. In this case, the walls of the small intestine wrap around the longitudinally extending wall 104 of the ingestible device 100, and the ingestible device 100 travels through the small intestine with one of the ends 102A or 102B in front.

[0371] For illustrative purposes, the ingestible device 100 of FIG. 1 shows the first opening 106 located in a portion of the wall 104 and oriented radially, and the second opening 108 located near the first end 102A and oriented longitudinally. However, in some embodiments, the exact location and orientation of the first opening 106 and the second opening 108 may be different from that shown in FIG. 1. During transit through the GI Tract, natural contractions within the small intestine may apply pressure radially to different portions of the wall 104 of the ingestible device 100, which may force solids or fluids into the first opening 106. As new material (e.g., fluid and solid particulates from the small intestine or other portions of the GI tract) enters the curved chamber 110 through the first opening 106, older material already located in the curved chamber 110 may be naturally forced out of the curved chamber 110 through the second opening 108.

[0372] In some embodiments, a portion of the curved chamber 110 may be used as a sampling chamber, which may hold samples obtained from the GI tract. In some embodiments the curved chamber 110 is subdivided into sub-chambers, each of which may be separated by a series of one or more valves or interlocks. For example, sub-chambers may be used to retain multiple samples within different portions of the curved chamber 110. In some embodiments, the curved chamber 110 is connected to other chambers within the ingestible device 100, or other openings located on the housing of the ingestible device 100. This may allow new samples to be acquired in the curved chamber 110 while older samples of interest are still stored within the ingestible device 100. In some embodiments, the ingestible device 100 is equipped with sensors to detect the properties a sample contained in the sampling chamber, or the results of an assay technique applied to the sample. In some embodiments, the ingestible device 100 is configured to obtain and retain a sample within the sampling chamber, which may be retrieved at a later time.

[0373] In some embodiments, the first opening 106, the second opening 108, or the curved chamber 110 include one or more of a hydrophilic or hydrophobic material, a sponge, a valve, or an air permeable membrane. For example, a one-way valve may prevent material from entering the curved chamber 110 through the second opening 108. As an alternate example, placing an air permeable membrane within the curved chamber 110 near the second opening 108 may allow unwanted gasses and air bubbles to pass through the air permeable membrane and exit the curved chamber 110, while solid or liquid samples may be prevented from passing through the air permeable membrane, and are retained within the curved chamber 110. The air permeable membrane may also prevent solid or liquid samples from entering the curved chamber 110 through the second opening 108.

[0374] The use of a hydrophilic material or sponge may allow samples to be retained within the curved chamber 110, and may reduce the amount of pressure needed for fluid to enter through the first opening 106 and dislodge air or gas in the curved chamber 110. Examples of hydrophilic materials that may be incorporated into the ingestible device 100 include hydrophilic polymers such as polyvinyl alcohol, polyvinyl pyrrolidone, and the like. Similarly, materials that have undergone various types of treatments, such as plasma treatments, may have suitable hydrophilic properties, and may be incorporated into the investible device 100. Sponges may be made of any suitable material or combination of materials, such as fibers of cotton, rayon, glass, polyester, polyethylene, polyurethane, and the like. Sponges generally may be made from commercially available materials, such as those produced by Porex ®< .

[0375] In some embodiments, the sponges may be treated in order to change their absorbency or to help preserve samples. Examples of materials which may be used to treat the sponges, alone or in combination, include sorbic acid, propyl parabene, citric acid, surfactants such as Tween ®< (polysorbate), DNA inhibitors and stabilizers, RNA inhibitors and stabilizers, protein inhibitors and stabilizers, and the like. In some embodiments, the sponges may be cut or abraded to change their absorbency or other physical properties.

[0376] Hydrophobic materials located near the second opening 108 may repel liquids, discouraging liquid samples from entering or exiting the curved chamber 110 through the second opening 108. This may serve a similar function as an air permeable membrane. Examples of hydrophobic materials which may be incorporated into the ingestible device 100 include polycarbonate, acrylics, fluorocarbons, styrenes, certain forms of vinyl, and the like.

[0377] The various materials listed above are provided as examples, and are not limiting. In practice, any type of suitable hydrophilic, hydrophobic, or sample preserving material may be used in the ingestible device 100, and the teachings discussed in relation to ingestible device 100 may be incorporated into any of the other ingestible devices described in this disclosure. Various methods for taking samples, controlling the movement of samples, or removing unwanted gasses, are discussed in detail in relation to FIGs. 2-9, and any of the various structures or techniques described in connection with FIGs. 2-9 may be incorporated into the ingestible device 100.

[0378] FIG. 2 illustrates an example ingestible device 200 with multiple openings in the housing and various modifications that may be made to the ingestible device 100 (FIG. 1). Similar to the ingestible device 100, the ingestible device 200 has an outer housing with a first end 202A, a second end 202B, and a wall 204 extending longitudinally from the first end 202A to the second end 202B. Also similar to the ingestible device 100, the ingestible device 200 has a first opening 206 in the housing, which is connected to a second opening 208 in the housing. The connection between the first opening 206 and the second opening 208 forms a curved chamber 210 within the ingestible device 200.

[0379] In the ingestible device 200, a portion of the curved chamber 210 forms a sampling chamber 212. In some embodiments, the ingestible device 200 may include a sensor (not shown) within or proximate to the sampling chamber. This sensor may be used to detect a property of the sample. In some embodiments, an assay technique is applied to a sample within the sampling chamber, and the sensor may be used to detect the results of the assay technique. A first valve 214 is located between the first opening 206 and the sampling chamber 212. Similarly, a second valve 216 is located between the second opening 208 and the sampling chamber 212. In some embodiments, the valves 214 and 216 prevent a fluid from entering or exiting the sampling chamber 212, or may be used to isolate a sample within the sampling chamber 212.

[0380] The ingestible device 200 includes a mechanical actuator 218 coupled to the valves 214 and 216. In some embodiments, the mechanical actuator 218 is used to move one or both of the valves 214 and 216 between an open and a closed position. In some embodiments, the mechanical actuator 218 is controlled by a microcontroller, microprocessor, or other circuitry inside the ingestible device 200. In an open position, the first valve 214 may allow a sample to pass in and out of the sampling chamber 212 through the portion of the curved chamber 210 connected to the first opening 206. Similarly, in an open position, the second valve 216 may allow a sample to pass in and out of the sampling chamber 212 from the portion of the curved chamber 210 connected to the second opening 208. When the valves 214 and 216 are in the closed positions, they may not allow a sample to pass into or out of the sampling chamber 212.

[0381] In some embodiments, the valves 214 and 216 are rotary valves, pin valves, flap valves, butterfly valves, ball valves, plug valves, or any other suitable type of one-way or two-way valves, and may be the same or different types of valves. In some embodiments, one or both of the valves 214 and 216 are automatic valves that reseal themselves after a sample has been obtained, similar to the osmotic valve mechanism discussed in relation to FIG. 3. In some embodiments, one or both of the valves 214 and 216 include a pumping mechanism, such as the pumping mechanism discussed in relation to FIG. 9. For illustrative purposes, the ingestible device 200 is depicted with both of the valves 214 and 216 as moveable two-way valves coupled to the mechanical actuator 218. However, in some embodiments, the mechanical actuator 218 is coupled to only one of the valves, and the other valve may be replaced with a passive one-way valve. For example, the mechanical actuator 218 may be coupled to only the first valve 214, and the second valve 216 may be replaced with a passive one-way valve that allows gases, fluids, or solids to exit the sampling chamber 212 through the portion of the curved chamber 210 connected to the second opening 208. This may restrict fluid from entering the sampling chamber 212 from the second opening 208, but allow unwanted material to be removed from the sampling chamber 212 as the sample is obtained.

[0382] In some embodiments, the ingestible device 200 may be able to detect the approximate location of the ingestible device 200 within the GI tract. For example, it may be possible to use various combinations of light emitting diodes and sensors positioned along the ingestible device 200 to determine whether the device is in the stomach, small intestine, or large intestine. Methods for determining the location of an ingestible device within a GI tract are described in greater detail elsewhere herein. In these embodiments, the ingestible device 200 may be configured to use the mechanical actuator 218 to move the valves 214 and 216 into an open position in response to determining that the ingestible device 200 has reached a predetermined location within the GI tract. For example, a microcontroller on board the ingestible device 200 may be configured to open the valves 214 and 216 only when the ingestible device 200 is within the small intestine, thereby obtaining a sample from within the small intestine.

[0383] For illustrative purposes, the ingestible device 200 is depicted with the mechanical actuator 218, the first valve 214, and the second valve 216 oriented in a substantially straight line, with a single shaft 220 being used to couple the mechanical actuator 218 to the valves 214 and 216. However, in some embodiments, the orientation and / or positioning of the valves 214 and 216 relative to the position of the mechanical actuator 218 may be different than that shown, and the coupling of the mechanical actuator 218 to the valves 214 and 216 may also be different. In some embodiments, the mechanical actuator 218 simultaneously moves the valves 214 and 216. For example, in some embodiments the valves 214 and 216 are rotary valves, and they may be simultaneously opened and closed by rotating the shaft 220 that extends from the mechanical actuator 218 along the length of the ingestible device 200. As an alternate example, the valves 214 and 216 may be pin valves, and the pins may be attached to the shaft 220 that extends from the mechanical actuator 218 along the length of the ingestible device 200. In this case, the mechanical actuator 218 may open and close the valves by moving the shaft 220 linearly. This may be accomplished either by configuring mechanical actuator 218 to be a linear actuator, such as a solenoid. Alternately, the mechanical actuator 218 may be a rotary actuator, and the rotation may be converted into a linear motion. One skilled in the art will understand that this may be done any number of ways, for example, by coupling the mechanical actuator 218 to a ball screw mechanism, a threaded lead nut and lead screw mechanism, a rack and pinion mechanism, or the like.

[0384] In some embodiments, the ingestible device 200 does not include the second valve 216 at all. In this case, fluids and solids contained within the sampling chamber 212 may be free to exit through the second opening 208. Alternately, the second valve 216 near the second opening 208 may be replaced by an air-permeable membrane, which may allow gasses and unwanted air bubbles to exit the sampling chamber 212 through the second opening 208, while still retaining fluids and / or solids within the sampling chamber 212. Alternately, the second valve 216 near the second opening 208 may be replaced with a hydrophobic material. Similar to an air permeable membrane, an appropriately positioned hydrophobic material may be used to line the walls of the curved chamber 210 proximate to the second opening 208, which may allow gasses or unwanted air bubbles to exit the sampling chamber 212 through the second opening 208, while restricting some fluids from entering or exiting the sampling chamber 212 through the second opening 208. In some embodiments, one or more of the above described mechanisms may be combined in the same ingestible device. For example, the ingestible device 200 may implement the second valve 216 as a two-way valve, and also have hydrophobic material and an air-permeable membrane located near the second opening 208.

[0385] In some embodiments, the curved chamber 210 is connected to one or more sub-chambers (not shown). Each of these sub-chambers may be configured to hold one or more samples, and isolate the samples from both the sampling chamber 212, and the other sub-chambers. For example, each sub-chamber may be connected to the curved chamber 210 through a one-way valve, allowing samples to enter the sub-chamber from the curved chamber 210, but preventing the obtained samples from exiting the sub-chamber and re-entering either the curved chamber 210 or the sampling chamber 212. In general, any type of valve or other suitable mechanism may be used to isolate samples contained in the sub-chambers. In some embodiments, the ingestible device 200 distributes different samples into different sub-chambers at different times, or from different locations of the GI tract. For example, the ingestible device 200 may obtain a sample from the duodenum and distribute it into a first sub-chamber, and the ingestible device 200 may later obtain a sample from the ileum and distribute it into a second sub-chamber. In some embodiments, different types of assay techniques or diagnostics are applied to some of the samples contained in the different sub-chambers.

[0386] FIG. 3 illustrates an example of an osmotic valve mechanism 300, which may be incorporated into an ingestible device in order to obtain samples. The osmotic valve mechanism 300 may be used in an ingestible device that features a first end, a second end, and a wall extending longitudinally between the first end and the second end, similar to the shape of the ingestible devices 100 (FIG. 1) and 200 (FIG. 2).

[0387] The osmotic valve mechanism 300 includes an inlet port 302, which is connected to a sampling chamber 304. In some embodiments, the inlet port 302 connects sampling chamber 304 directly or indirectly to an opening in the housing of an ingestible device.

[0388] The initial state of the osmotic valve mechanism 300 is shown in diagram 300A. As shown in diagram 300A, the inlet port 302 of the osmotic valve mechanism 300 is sealed using a single use sealing device 306 positioned within the inlet port 302. The single use sealing device 306 is positioned adjacent to a heating element 308. When it is time for the osmotic valve mechanism 300 to be opened (which may be determined by a localization mechanism that determines the ingestible device is located in a desirable portion of the GI tract), the heating element 308 applies heat to the sealing device 306, causing the sealing device 306 to deform and unseal the inlet port 302.

[0389] In some embodiments, the sealing device 306 may be a plug made out of a material that is meltable, deformable, and / or destroyable through the use of the heating element 308, such as wax. For example, in some embodiments, the heating element 308 may be a resistive heater that undergoes ohmic heating as an electrical current is passed through it, and the sealing device 306 is a wax plug. In some embodiments, the type of wax used to form the wax plug has a melting point between 38 degrees and 80 degrees Celsius, which is above the ambient temperature of a human body, but which may be easily achieved using the heating element 308. Some embodiments of the osmotic valve mechanism 300 may use a sealing device 306 that is melted or deformed at temperatures outside of the range described above, but practical considerations may be made to ensure that the osmotic valve mechanism 300 does not cause unwanted damage or burning to the GI tract. In some embodiments, a microprocessor is configured to control the heating element 308, causing it to generate heat. For example, the microprocessor may be configured to activate the heating element 308 once the ingestible device reaches a particular location within the GI tract. An example mechanism for unsealing the inlet port 302 is described in greater detail in relation to FIGs. 4 and 5. Although FIGs. 3, 4, and 5 depict the sealing device 306 as a type of plug, any type of suitable sealing device may be used. For example, in some embodiments, the sealing device includes a breakable membrane, which may be destroyed when heat is applied to the membrane. In some embodiments, the osmotic valve mechanism 300 does not include a heating element 308, and the sealing device 306 is melted, deformed, destroyed, or dislodged from the inlet port 302 by a mechanical actuator, or through electromagnetic fields. For example, the sealing device 306 may be a membrane that will rupture when a sufficiently large electrical current or magnetic field is applied to the membrane.

[0390] Inside the sampling chamber 304 of the osmotic valve mechanism 300 is made of a member including an absorptive material 310, and at least a portion of the absorptive material 310 is located near the inlet port 302. Th...

Claims

1. A pharmaceutical formulation for use in a method for treating small intestinal bacterial overgrowth (SIBO) in a subject in need thereof, the method comprising: orally administering an effective amount of the pharmaceutical formulation, which comprises an antimicrobial agent, to the subject, thereby treating SIBO in the subject, wherein the antimicrobial agent is meropenem or ceftriaxone and wherein the pharmaceutical formulation is either: formulated for oral administration as a solid dosage form with an enteric coating; or is administered in an ingestible device and released into the small intestine.

2. The pharmaceutical formulation for the use according to claim 1, wherein the antimicrobial agent exhibits antimicrobial activity against a bacterium implicated in the pathogenesis of SIBO with either a MIC50 or a MIC90 value of 0.001 µg / mL to 64 µg / mL, 0.004 µg / mL to 32 µg / mL, 0.015 µg / mL to 16 µg / mL, 0.03 µg / mL to 8 µg / mL, or 0.5 µg / mL to 2 µg / mL.

3. The pharmaceutical formulation for the use according to claim 1 or claim 2, wherein the antimicrobial agent exhibits antimicrobial activity against a bacterium implicated in the pathogenesis of SIBO with a MIC range of 0.001 µg / mL to 128 µg / mL, 0.001 µg / mL to 64 µg / mL, 0.004 µg / mL to 32 µg / mL, 0.015 µg / mL to 16 µg / mL, 0.03 µg / mL to 8 µg / mL, or 0.5 µg / mL to 2 µg / mL, and / or wherein the bacterium is selected from the group consisting of a gram-positive bacterium, a gram-negative bacterium, an anaerobic bacterium, and combinations thereof.

4. The pharmaceutical formulation for the use according to claim 2 or claim 3 , wherein the bacterium is selected from the group consisting of Enterobacter aerogenes, Escherichia coli, Klebsiella spp., K. oxytoca, K. pneumonia, Proteus mirabilis, Pseudomonas aeruginosa, Staphylococcus aureus, Enterococcus faecalis, Streptococcus spp., Streptococcus pyogenes, Streptococcus agalactiae, Viridans group Streptococcus, Clostridium spp., C. sporogenes, C. ramosum, C. innocuum, Prevotella spp., P. melanogenica, P. bivia, P. buccae, P. nanceiensis, P. intermedia, P. denticola, P. nigrescens, P. corporis, P. bergensis, P. disiens, Veillonella spp., V. parvula, Veillonella dispr, V. atypica, Bacteroides fragilis, Bacteroides non-fragilis, B. caccae, B. thetaiotaomicron, B. ovatus, B. vulgatus, B. uniformis, B. stercoris, B. xylanisolvens, B salyersiae, B. intestinalis, and B. faecis, and / or wherein the antimicrobial agent exhibits bactericidal efficacy against the bacterium.

5. The pharmaceutical formulation for the use according to claim 4, wherein the antimicrobial agent exhibits bactericidal efficacy against the bacterium at a concentration of 0.5X MIC to 8X MIC, 1X MIC to 6X MIC, or 2X MIC to 4X MIC, and / or wherein the antimicrobial agent exhibits bactericidal efficacy of at least a 3-log reduction in colony forming units (CFU) per mL in 2 hours, 6 hours, 24 hours, or 48 hours.

6. The pharmaceutical formulation for the use according to any one of claims 4-5, wherein the antimicrobial agent exhibits a minimum 3-log reduction in CFU / mL of E. coli, Streptococcus spp., Bacteroides spp, or any combination thereof, after 24 hours of exposure to the antimicrobial agent, and / or wherein exposure of the bacterium to the antimicrobial agent prevents regrowth of the bacterium.

7. The pharmaceutical formulation for the use according to any one of claims 2-6, wherein the bacterium has a spontaneous mutation frequency of less than 7.45×10-9, 5.75×10-9, 5.15 × 10-9, 9.55× 10-10, 1.85× 10-10, 1.75× 10-10, 1.50× 10-10, or 1.05 ×10-10, and / or wherein the antimicrobial agent exhibits a mutation prevention concentration of 0.01 µg / mL to 32 µg / mL, 0.05 µg / mL to 1 µg / mL, or 0.1 µg / mL to 0.25 µg / mL against the bacterium.

8. The pharmaceutical formulation for the use according to claim 7, wherein the bacterium is selected from the group consisting of Escherichia coli, Streptococcus spp., Bacteroides spp., and combinations thereof, optionally wherein the bacterium is selected from the group consisting of E. coli, B. fragilis, B. vulgatus, B. ovatus, S. pneumonia, S. pyogenes, and S. agalactiae, and combinations thereof.

9. A pharmaceutical formulation for use in a method of preventing regrowth of a bacterium implicated in the pathogenesis of SIBO in a subject in need thereof, the method comprising: orally administering an effective amount of the pharmaceutical formulation, which comprises an antimicrobial agent, to the subject, wherein the antimicrobial agent exhibits antimicrobial activity against a bacterium implicated in the pathogenesis of SIBO; and decreasing the amount of bacterium by at least a 3-log reduction in CFU / mL, as compared to the amount of bacterium at the time of beginning administration of the formulation, wherein exposure of the bacterium to the antimicrobial agent prevents regrowth of the bacterium, optionally wherein the bacterium is selected from the group consisting of E. coli, Streptococcus spp., Bacteroides spp, or any combination thereof, wherein the antimicrobial agent is selected from meropenem and ceftriaxone and wherein the pharmaceutical formulation is either: formulated for oral administration as a solid dosage form with an enteric coating; or is administered in an ingestible device and released into the small intestine.

10. A pharmaceutical formulation for use in a method of preventing the development of resistance to treatment by an antimicrobial agent of a bacterium implicated in the pathogenesis of SIBO in a subject in need thereof, the method comprising: orally administering an effective amount of the pharmaceutical formulation, which comprises the antimicrobial agent, to the subject, wherein the antimicrobial agent is meropenem or ceftriaxone, wherein the pharmaceutical formulation is either: formulated for oral administration as a solid dosage form with an enteric coating; or is administered in an ingestible device and released into the small intestine, and wherein the bacterium has a spontaneous mutation frequency of less than 7.45×10-9, 5.75×10-9, 5.15× 10-9, 9.55×10-10, 1.85×10-10, 1.75× 10-10, 1.50×10-10, or 1.05×10-10.

11. The pharmaceutical formulation for the use according to claim 10, wherein the antimicrobial agent exhibits a mutation prevention concentration of 0.01 µg / mL to 32 µg / mL, 0.05 µg / mL to 1 µg / mL, or 0.1 µg / mL to 0.25 µg / mL against the bacterium.

12. The pharmaceutical formulation for the use according to claim 10 or 11, wherein the bacterium is selected from the group consisting of Escherichia coli, Streptococcus spp., Bacteroides spp., and combinations thereof.

13. The pharmaceutical formulation for the use according to claim 12, wherein the bacterium is selected from the group consisting of E. coli, B. fragilis, B. vulgatus, B. ovatus, S. pneumonia, S. pyogenes, and S. agalactiae, and combinations thereof.

14. The pharmaceutical formulation for the use according to any one of claims 10-13, wherein the antimicrobial agent is meropenem.