The Human Microbiota in Health and Disease

O’Hara, 2006, The gut flora as a forgotten organ, EMBO Rep, 7, 688, 10.1038/sj.embor.7400731 Ursell, 2014, The intestinal metabolome: an intersection between microbiota and host, Gastroenterology, 146, 1470, 10.1053/j.gastro.2014.03.001 Whitman, 1998, Prokaryotes: the unseen majority, Proc Natl Acad Sci USA, 95, 6578, 10.1073/pnas.95.12.6578 Savage, 1977, Microbial ecology of the gastrointestinal tract, Annu Rev Microbiol, 31, 107, 10.1146/annurev.mi.31.100177.000543 Ley, 2006, Ecological and evolutionary forces shaping microbial diversity in the human intestine, Cell, 124, 837, 10.1016/j.cell.2006.02.017 Wang, 2015, Who determines the outcomes of HBV exposure?, Trends Microbiol, 23, 328, 10.1016/j.tim.2015.04.001 Ley, 2006, Microbial ecology: human gut microbes associated with obesity, Nature, 444, 1022, 10.1038/4441022a Wang, 2016, Altered fecal microbiota correlates with liver biochemistry in nonobese patients with non-alcoholic fatty liver disease, Sci Rep, 6 Gill, 2006, Metagenomic analysis of the human distal gut microbiome, Science, 312, 1355, 10.1126/science.1124234 Roberfroid, 1995, Colonic microflora: nutrition and health. Summary and conclusions of an International Life Sciences Institute (ILSI) [Europe] workshop held in Barcelona, Spain, Nutr Rev, 53, 127, 10.1111/j.1753-4887.1995.tb01535.x Cash, 2006, Symbiotic bacteria direct expression of an intestinal bactericidal lectin, Science, 313, 1126, 10.1126/science.1127119 Hooper, 2003, Angiogenins: a new class of microbicidal proteins involved in innate immunity, Nat Immunol, 4, 269, 10.1038/ni888 Schauber, 2003, Expression of the cathelicidin LL-37 is modulated by short chain fatty acids in colonocytes: relevance of signalling pathways, Gut, 52, 735, 10.1136/gut.52.5.735 Bouskra, 2008, Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis, Nature, 456, 507, 10.1038/nature07450 Rakoff-Nahoum, 2008, Innate immune recognition of the indigenous microbial flora, Mucosal Immunol, 1, S10, 10.1038/mi.2008.49 Macpherson, 2004, Interactions between commensal intestinal bacteria and the immune system, Nat Rev Immunol, 4, 478, 10.1038/nri1373 Sekirov, 2010, Gut microbiota in health and disease, Physiol Rev, 90, 859, 10.1152/physrev.00045.2009 Sartor, 2008, Microbial influences in inflammatory bowel diseases, Gastroenterology, 134, 577, 10.1053/j.gastro.2007.11.059 Liu, 2004, Synbiotic modulation of gut flora: effect on minimal hepatic encephalopathy in patients with cirrhosis, Hepatology, 39, 1441, 10.1002/hep.20194 Scanlan, 2008, Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis, Environ Microbiol, 10, 789, 10.1111/j.1462-2920.2007.01503.x Verhulst, 2008, A longitudinal analysis on the association between antibiotic use, intestinal microflora, and wheezing during the first year of life, J Asthma, 45, 828, 10.1080/02770900802339734 Finegold, 2002, Gastrointestinal microflora studies in late-onset autism, Clin Infect Dis, 35, S6, 10.1086/341914 Wen, 2008, Innate immunity and intestinal microbiota in the development of Type 1 diabetes, Nature, 455, 1109, 10.1038/nature07336 Turnbaugh, 2006, An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 444, 1027, 10.1038/nature05414 Perry, 2016, Acetate mediates a microbiome-brain-β-cell axis to promote metabolic syndrome, Nature, 534, 213, 10.1038/nature18309 Cani, 2004, Inulin-type fructans modulate gastrointestinal peptides involved in appetite regulation (glucagon-like peptide-1 and ghrelin) in rats, Br J Nutr, 92, 521, 10.1079/BJN20041225 Hollister, 2014, Compositional and functional features of the gastrointestinal microbiome and their effects on human health, Gastroenterology, 146, 1449, 10.1053/j.gastro.2014.01.052 Rogier, 2014, Lessons from mother: long-term impact of antibodies in breast milk on the gut microbiota and intestinal immune system of breastfed offspring, Gut Microbes, 5, 663, 10.4161/19490976.2014.969984 Round, 2009, The gut microbiota shapes intestinal immune responses during health and disease, Nat Rev Immunol, 9, 313, 10.1038/nri2515 Larsbrink, 2014, A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes, Nature, 506, 498, 10.1038/nature12907 Goh, 2015, Genetic mechanisms of prebiotic oligosaccharide metabolism in probiotic microbes, Annu Rev Food Sci Technol, 6, 137, 10.1146/annurev-food-022814-015706 Morowitz, 2011, Contributions of intestinal bacteria to nutrition and metabolism in the critically ill, Surg Clin North Am, 91, 771, 10.1016/j.suc.2011.05.001 Duncan, 2009, The role of pH in determining the species composition of the human colonic microbiota, Environ Microbiol, 11, 2112, 10.1111/j.1462-2920.2009.01931.x Cani, 2013, Gut microbiota, enteroendocrine functions and metabolism, Curr Opin Pharmacol, 13, 935, 10.1016/j.coph.2013.09.008 Flint, 2012, The role of the gut microbiota in nutrition and health, Nat Rev Gastroenterol Hepatol, 9, 577, 10.1038/nrgastro.2012.156 Kang, 2012, Recent advances in microbial production of δ-aminolevulinic acid and vitamin B12, Biotechnol Adv, 30, 1533, 10.1016/j.biotechadv.2012.04.003 Cebra, 1999, Influences of microbiota on intestinal immune system development, Am J Clin Nutr, 69, 1046S, 10.1093/ajcn/69.5.1046s Thaiss, 2016, The microbiome and innate immunity, Nature, 535, 65, 10.1038/nature18847 Madsen, 1999, Lactobacillus species prevents colitis in interleukin 10 gene-deficient mice, Gastroenterology, 116, 1107, 10.1016/S0016-5085(99)70013-2 Magrone, 2013, The interplay between the gut immune system and microbiota in health and disease: nutraceutical intervention for restoring intestinal homeostasis, Curr Pharm Des, 19, 1329 Brenchley, 2012, Microbial translocation across the GI tract, Annu Rev Immunol, 30, 149, 10.1146/annurev-immunol-020711-075001 Hand, 2012, Acute gastrointestinal infection induces long-lived microbiota-specific T cell responses, Science, 337, 1553, 10.1126/science.1220961 Ling, 2015, Decreased diversity of the oral microbiota of patients with hepatitis B virus-induced chronic liver disease: a pilot report, Sci Rep, 5, 10.1038/srep17098 Cohen, 2016, Vaginal microbiome affects HIV risk, Science, 353, 331, 10.1126/science.353.6297.331 Gu, 2016, Identification of key taxa that favor intestinal colonization of Clostridium difficile in an adult Chinese population, Microbes Infect, 18, 30, 10.1016/j.micinf.2015.09.008 Ling, 2014, Impacts of infection with different toxigenic Clostridium difficile strains on faecal microbiota in children, Sci Rep, 4, 7485, 10.1038/srep07485 Ling, 2016, Alterations in the fecal microbiota of patients with HIV-1 infection: an observational study in a Chinese population, Sci Rep, 6, 10.1038/srep30673 Xu, 2012, Changes of fecal Bifidobacterium species in adult patients with hepatitis B virus-induced chronic liver disease, Microb Ecol, 63, 304, 10.1007/s00248-011-9925-5 Hu, 2016, Effect of Helicobacter pylori infection on chronic periodontitis by the change of microecology and inflammation, Oncotarget, 7, 66700, 10.18632/oncotarget.11449 Ling, 2010, Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis, BMC Genomics, 11, 488, 10.1186/1471-2164-11-488 Giannelli, 2014, Microbiota and the gut-liver axis: bacterial translocation, inflammation and infection in cirrhosis, World J Gastroenterol, 20, 16795, 10.3748/wjg.v20.i45.16795 Nardone, 2004, Probiotics: a potential target for the prevention and treatment of steatohepatitis, J Clin Gastroenterol, 38, S121, 10.1097/01.mcg.0000128934.53920.1d Cesaro, 2011, Gut microbiota and probiotics in chronic liver diseases, Dig Liver Dis, 43, 431, 10.1016/j.dld.2010.10.015 Lakshmi, 2010, Frequency and factors associated with small intestinal bacterial overgrowth in patients with cirrhosis of the liver and extra hepatic portal venous obstruction, Dig Dis Sci, 55, 1142, 10.1007/s10620-009-0826-0 Gupta, 2010, Role of small intestinal bacterial overgrowth and delayed gastrointestinal transit time in cirrhotic patients with minimal hepatic encephalopathy, J Hepatol, 53, 849, 10.1016/j.jhep.2010.05.017 Chen, 2011, Characterization of fecal microbial communities in patients with liver cirrhosis, Hepatology, 54, 562, 10.1002/hep.24423 Qin, 2014, Alterations of the human gut microbiome in liver cirrhosis, Nature, 513, 59, 10.1038/nature13568 Chen, 2016, Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology, Sci Rep, 6 Chen, 2015, Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality, J Gastroenterol Hepatol, 30, 1429, 10.1111/jgh.12932 Dapito, 2012, Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4, Cancer Cell, 21, 504, 10.1016/j.ccr.2012.02.007 Ozaslan, 2016, Further considerations in autoimmune hepatitis, J Hepatol, 64, 1457, 10.1016/j.jhep.2015.12.027 Marchesi, 2016, The gut microbiota and host health: a new clinical frontier, Gut, 65, 330, 10.1136/gutjnl-2015-309990 Lv, 2016, Alterations and correlations of the gut microbiome, metabolism and immunity in patients with primary biliary cirrhosis, Environ Microbiol, 18, 2272, 10.1111/1462-2920.13401 Björnsson, 2005, Intestinal permeability and bacterial growth of the small bowel in patients with primary sclerosing cholangitis, Scand J Gastroenterol, 40, 1090, 10.1080/00365520510023288 Tilg, 2017, NAFLD and diabetes mellitus, Nat Rev Gastroenterol Hepatol, 14, 32, 10.1038/nrgastro.2016.147 Wesolowski SR, Kasmi KC, Jonscher KR, Friedman JE. Developmental origins of NAFLD: a womb with a clue. Nat Rev Gastroenterol Hepatol. Epub 2016 Oct 26. Boursier, 2016, The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota, Hepatology, 63, 764, 10.1002/hep.28356 de Martel, 2012, Global burden of cancers attributable to infections in 2008: a review and synthetic analysis. Lancet Oncol, 13, 607 Wong, 2004, Helicobacter pylori eradication to prevent gastric cancer in a high-risk region of China: a randomized controlled trial, JAMA, 291, 187, 10.1001/jama.291.2.187 Herrera, 2009, Helicobacter pylori and gastric adenocarcinoma, Clin Microbiol Infect, 15, 971, 10.1111/j.1469-0691.2009.03031.x El-Omar, 2000, Interleukin-1 polymorphisms associated with increased risk of gastric cancer, Nature, 404, 398, 10.1038/35006081 de Sablet, 2011, Phylogeographic origin of Helicobacter pylori is a determinant of gastric cancer risk, Gut, 60, 1189, 10.1136/gut.2010.234468 Rhead, 2007, A new Helicobacter pylori vacuolating cytotoxin determinant, the intermediate region, is associated with gastric cancer, Gastroenterology, 133, 926, 10.1053/j.gastro.2007.06.056 Cover, 2003, Induction of gastric epithelial cell apoptosis by Helicobacter pylori vacuolating cytotoxin, Cancer Res, 63, 951 Oertli, 2012, DC-derived IL-18 drives Treg differentiation, murine Helicobacter pylori-specific immune tolerance, and asthma protection, J Clin Invest, 122, 1082, 10.1172/JCI61029 Blaser, 1995, Infection with Helicobacter pylori strains possessing cagA is associated with an increased risk of developing adenocarcinoma of the stomach, Cancer Res, 55, 2111 Kaparakis, 2010, Bacterial membrane vesicles deliver peptidoglycan to NOD1 in epithelial cells, Cell Microbiol, 12, 372, 10.1111/j.1462-5822.2009.01404.x Odenbreit, 2000, Translocation of Helicobacter pylori cagA into gastric epithelial cells by type IV secretion, Science, 287, 1497, 10.1126/science.287.5457.1497 Lertpiriyapong, 2014, Gastric colonisation with a restricted commensal microbiota replicates the promotion of neoplastic lesions by diverse intestinal microbiota in the Helicobacter pylori INS-GAS mouse model of gastric carcinogenesis, Gut, 63, 54, 10.1136/gutjnl-2013-305178 Sanapareddy, 2012, Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans, ISME J, 6, 1858, 10.1038/ismej.2012.43 Castellarin, 2012, Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma, Genome Res, 22, 299, 10.1101/gr.126516.111 Zackular, 2013, The gut microbiome modulates colon tumorigenesis, MBio, 4, e00692, 10.1128/mBio.00692-13 Keku, 2013, Fusobacterium spp. and colorectal cancer: cause or consequence, Trends Microbiol, 21, 506, 10.1016/j.tim.2013.08.004 Feng, 2015, Gut microbiome development along the colorectal adenoma-carcinoma sequence, Nat Commun, 6, 6528, 10.1038/ncomms7528 Rubinstein, 2013, Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-cadherin/β-catenin signaling via its FadA adhesin, Cell Host Microbe, 14, 195, 10.1016/j.chom.2013.07.012 Kostic, 2013, Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment, Cell Host Microbe, 14, 207, 10.1016/j.chom.2013.07.007 Sokol, 1999, Wnt signaling and dorso-ventral axis specification in vertebrates, Curr Opin Genet Dev, 9, 405, 10.1016/S0959-437X(99)80061-6 Sears, 2009, Enterotoxigenic Bacteroides fragilis: a rogue among symbiotes, Clin Microbiol Rev, 22, 349, 10.1128/CMR.00053-08 Shiryaev, 2013, Substrate cleavage profiling suggests a distinct function of Bacteroides fragilis metalloproteinases (fragilysin and metalloproteinase II) at the microbiome-inflammation-cancer interface, J Biol Chem, 288, 34956, 10.1074/jbc.M113.516153 Wu, 2009, A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses, Nat Med, 15, 1016, 10.1038/nm.2015 Huycke, 2002, Enterococcus faecalis produces extracellular superoxide and hydrogen peroxide that damages colonic epithelial cell DNA, Carcinogenesis, 23, 529, 10.1093/carcin/23.3.529 Cuevas-Ramos, 2010, Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells, Proc Natl Acad Sci USA, 107, 11537, 10.1073/pnas.1001261107 Howe, 1992, Dietary intake of fiber and decreased risk of cancers of the colon and rectum: evidence from the combined analysis of 13 case-control studies, J Natl Cancer Inst, 84, 1887, 10.1093/jnci/84.24.1887 Clausen, 1991, Colonic fermentation of dietary fibre to short chain fatty acids in patients with adenomatous polyps and colonic cancer, Gut, 32, 923, 10.1136/gut.32.8.923 Singh, 2014, Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis, Immunity, 40, 128, 10.1016/j.immuni.2013.12.007 Lagergren, 1999, Symptomatic gastroesophageal reflux as a risk factor for esophageal adenocarcinoma, N Engl J Med, 340, 825, 10.1056/NEJM199903183401101 Lagergren, 2005, Adenocarcinoma of oesophagus: what exactly is the size of the problem and who is at risk?, Gut, 54, i1, 10.1136/gut.2004.041517 Anderson, 2008, Relationship between Helicobacter pylori infection and gastric atrophy and the stages of the oesophageal inflammation, metaplasia, adenocarcinoma sequence: results from the FINBAR case-control study, Gut, 57, 734, 10.1136/gut.2007.132662 Pei, 2004, Bacterial biota in the human distal esophagus, Proc Natl Acad Sci USA, 101, 4250, 10.1073/pnas.0306398101 Yang, 2009, Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome, Gastroenterology, 137, 588, 10.1053/j.gastro.2009.04.046 Finlay, 1982, Microbial flora in carcinoma of oesophagus, Thorax, 37, 181, 10.1136/thx.37.3.181 El-Serag, 1998, Opposing time trends of peptic ulcer and reflux disease, Gut, 43, 327, 10.1136/gut.43.3.327 Hamada, 2000, High incidence of reflux oesophagitis after eradication therapy for Helicobacter pylori: impacts of hiatal hernia and corpus gastritis, Aliment Pharmacol Ther, 14, 729, 10.1046/j.1365-2036.2000.00758.x Sommer, 2013, The gut microbiota—masters of host development and physiology, Nat Rev Microbiol, 11, 227, 10.1038/nrmicro2974 Franks, 2016, Exposing the exposures responsible for type 2 diabetes and obesity, Science, 354, 69, 10.1126/science.aaf5094 Le Chatelier, 2013, Richness of human gut microbiome correlates with metabolic markers, Nature, 500, 541, 10.1038/nature12506 Turnbaugh, 2009, A core gut microbiome in obese and lean twins, Nature, 457, 480, 10.1038/nature07540 Ridaura, 2013, Gut microbiota from twins discordant for obesity modulate metabolism in mice, Science, 341, 10.1126/science.1241214 David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature, 505, 559, 10.1038/nature12820 Caesar, 2015, Crosstalk between gut microbiota and dietary lipids aggravates WAT inflammation through TLR signaling, Cell Metab, 22, 658, 10.1016/j.cmet.2015.07.026 Sonnenburg, 2016, Diet-microbiota interactions as moderators of human metabolism, Nature, 535, 56, 10.1038/nature18846 Leone, 2015, Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism, Cell Host Microbe, 17, 681, 10.1016/j.chom.2015.03.006 Thaiss, 2014, Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis, Cell, 159, 514, 10.1016/j.cell.2014.09.048 Tremaroli, 2012, Functional interactions between the gut microbiota and host metabolism, Nature, 489, 242, 10.1038/nature11552 de Vos, 2013, Genomics: a gut prediction, Nature, 498, 48, 10.1038/nature12251 Delzenne, 2008, Gut microflora is a key player in host energy homeostasis, Med Sci (Paris), 24, 505, 10.1051/medsci/2008245505 Wahlström, 2016, Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism, Cell Metab, 24, 41, 10.1016/j.cmet.2016.05.005 Camilleri, 2015, Peripheral mechanisms in appetite regulation, Gastroenterology, 148, 1219, 10.1053/j.gastro.2014.09.016 Qin, 2012, A metagenome-wide association study of gut microbiota in type 2 diabetes, Nature, 490, 55, 10.1038/nature11450 Karlsson, 2013, Gut metagenome in European women with normal, impaired and diabetic glucose control, Nature, 498, 99, 10.1038/nature12198 Forslund, 2015, Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota, Nature, 528, 262, 10.1038/nature15766 Burcelin, 2016, Gut microbiota and immune crosstalk in metabolic disease, Mol Metab, 5, 771, 10.1016/j.molmet.2016.05.016 Pedersen, 2016, Human gut microbes impact host serum metabolome and insulin sensitivity, Nature, 535, 376, 10.1038/nature18646 Mardinoglu, 2016, Confounding effects of metformin on the human gut microbiome in type 2 diabetes, Cell Metab, 23, 10, 10.1016/j.cmet.2015.12.012 Wang, 2011, Low relative abundances of the mucolytic bacterium Akkermansia muciniphila and Bifidobacterium spp. in feces of children with autism, Appl Environ Microbiol, 77, 6718, 10.1128/AEM.05212-11 Ling, 2014, Altered fecal microbiota composition associated with food allergy in infants, Appl Environ Microbiol, 80, 2546, 10.1128/AEM.00003-14 Saarinen, 2005, Clinical course and prognosis of cow’s milk allergy are dependent on milk-specific IgE status, J Allergy Clin Immunol, 116, 869, 10.1016/j.jaci.2005.06.018 Bunyavanich, 2016, Early-life gut microbiome composition and milk allergy resolution, J Allergy Clin Immunol, 138, 1122, 10.1016/j.jaci.2016.03.041 Tomova, 2015, Gastrointestinal microbiota in children with autism in Slovakia, Physiol Behav, 138, 179, 10.1016/j.physbeh.2014.10.033 Jiang, 2015, Altered fecal microbiota composition in patients with major depressive disorder, Brain Behav Immun, 48, 186, 10.1016/j.bbi.2015.03.016 Russell, 2012, Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma, EMBO Rep, 13, 440, 10.1038/embor.2012.32 van Nimwegen, 2011, Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy, J Allergy Clin Immunol, 128, 948, 10.1016/j.jaci.2011.07.027 Atarashi, 2011, Induction of colonic regulatory T cells by indigenous Clostridium species, Science, 331, 337, 10.1126/science.1198469 Charlson, 2016, The burden of mental, neurological, and substance use disorders in China and India: a systematic analysis of community representative epidemiological studies, Lancet, 388, 376, 10.1016/S0140-6736(16)30590-6 Kendler, 2013, What psychiatric genetics has taught us about the nature of psychiatric illness and what is left to learn, Mol Psychiatry, 18, 1058, 10.1038/mp.2013.50 Maes, 2011, Depression is an inflammatory disease, but cell-mediated immune activation is the key component of depression, Prog Neuropsychopharmacol Biol Psychiatry, 35, 664, 10.1016/j.pnpbp.2010.06.014 Schmitt, 2014, The impact of environmental factors in severe psychiatric disorders, Front Neurosci, 8, 19, 10.3389/fnins.2014.00019 Cryan, 2012, Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour, Nat Rev Neurosci, 13, 701, 10.1038/nrn3346 Maes, 2012, Increased IgA and IgM responses against gut commensals in chronic depression: further evidence for increased bacterial translocation or leaky gut, J Affect Disord, 141, 55, 10.1016/j.jad.2012.02.023 Maes, 2013, In depression, bacterial translocation may drive inflammatory responses, oxidative and nitrosative stress (O&NS), and autoimmune responses directed against O&NS-damaged neoepitopes, Acta Psychiatr Scand, 127, 344, 10.1111/j.1600-0447.2012.01908.x Gosalbes, 2011, Metatranscriptomic approach to analyze the functional human gut microbiota, PLoS One, 6, 10.1371/journal.pone.0017447 Franzosa, 2014, Relating the metatranscriptome and metagenome of the human gut, Proc Natl Acad Sci USA, 111, E2329, 10.1073/pnas.1319284111 Santiago-Rodriguez, 2015, Transcriptome analysis of bacteriophage communities in periodontal health and disease, BMC Genomics, 16, 549, 10.1186/s12864-015-1781-0 Arnold, 2016, Emerging technologies for gut microbiome research, Trends Microbiol, 24, 887, 10.1016/j.tim.2016.06.008 Connon, 2002, High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates, Appl Environ Microbiol, 68, 3878, 10.1128/AEM.68.8.3878-3885.2002 Nichols, 2010, Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species, Appl Environ Microbiol, 76, 2445, 10.1128/AEM.01754-09 Jung, 2014, Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia, FEMS Microbiol Ecol, 90, 417 Possemiers, 2004, PCR-DGGE-based quantification of stability of the microbial community in a simulator of the human intestinal microbial ecosystem, FEMS Microbiol Ecol, 49, 495, 10.1016/j.femsec.2004.05.002 Petrof, 2014, From stool transplants to next-generation microbiota therapeutics, Gastroenterology, 146, 1573, 10.1053/j.gastro.2014.01.004 McDonald, 2015, Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model, J Microbiol Methods, 108, 36, 10.1016/j.mimet.2014.11.007 Wang, 2014, Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption, Nat Biotechnol, 32, 473, 10.1038/nbt.2857 Kim, 2012, Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow, Lab Chip, 12, 2165, 10.1039/c2lc40074j Rusconi, 2014, Microfluidics expanding the frontiers of microbial ecology, Annu Rev Biophys, 43, 65, 10.1146/annurev-biophys-051013-022916 Englert, 2010, Investigation of bacterial chemotaxis in flow-based microfluidic devices, Nat Protoc, 5, 864, 10.1038/nprot.2010.18 Wang, 2014, In vitro generation of colonic epithelium from primary cells guided by microstructures, Lab Chip, 14, 1622, 10.1039/C3LC51353J Gracz, 2015, A high-throughput platform for stem cell niche co-cultures and downstream gene expression analysis, Nat Cell Biol, 17, 340, 10.1038/ncb3104 Forbester, 2015, Interaction of Salmonella enterica serovar Typhimurium with intestinal organoids derived from human induced pluripotent stem cells, Infect Immun, 83, 2926, 10.1128/IAI.00161-15 Leslie, 2015, Persistence and toxin production by Clostridium difficile within human intestinal organoids result in disruption of epithelial paracellular barrier function, Infect Immun, 83, 138, 10.1128/IAI.02561-14 Sommer, 2015, Advancing gut microbiome research using cultivation, Curr Opin Microbiol, 27, 127, 10.1016/j.mib.2015.08.004 Dao, 2016, Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology, Gut, 65, 426, 10.1136/gutjnl-2014-308778 Chu, 2016, Discovery of MRSA active antibiotics using primary sequence from the human microbiome, Nat Chem Biol, 12, 1004, 10.1038/nchembio.2207 Wang, 2016, Metagenome-wide association studies: fine-mining the microbiome, Nat Rev Microbiol, 14, 508, 10.1038/nrmicro.2016.83 Lu, 2011, Intestinal microbiota was assessed in cirrhotic patients with hepatitis B virus infection. Intestinal microbiota of HBV cirrhotic patients, Microb Ecol, 61, 693, 10.1007/s00248-010-9801-8 Lu, 2014, An analysis of microbiota-targeted therapies in patients with avian influenza virus subtype H7N9 infection, BMC Infect Dis, 14, 359, 10.1186/1471-2334-14-359 van Nood, 2013, Duodenal infusion of donor feces for recurrent Clostridium difficile, N Engl J Med, 368, 407, 10.1056/NEJMoa1205037 Dhiman, 2014, Probiotic VSL#3 reduces liver disease severity and hospitalization in patients with cirrhosis: a randomized, controlled trial, Gastroenterology, 147, 1327, 10.1053/j.gastro.2014.08.031 Lv, 2014, Administration of Lactobacillus salivarius LI01 or Pediococcus pentosaceus LI05 improves acute liver injury induced by D-galactosamine in rats, Appl Microbiol Biotechnol, 98, 5619, 10.1007/s00253-014-5638-2 Atarashi, 2013, Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota, Nature, 500, 232, 10.1038/nature12331 Iida, 2013, Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment, Science, 342, 967, 10.1126/science.1240527 Viaud, 2013, The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide, Science, 342, 971, 10.1126/science.1240537 West, 2016, Probiotics for treatment and primary prevention of allergic diseases and asthma: looking back and moving forward, Expert Rev Clin Immunol, 12, 625, 10.1586/1744666X.2016.1147955