{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T18:40:20Z","timestamp":1793040020544,"version":"4.5.0"},"reference-count":113,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2021,10,1]],"date-time":"2021-10-01T00:00:00Z","timestamp":1633046400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,10,1]],"date-time":"2021-10-01T00:00:00Z","timestamp":1633046400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,8,11]],"date-time":"2021-08-11T00:00:00Z","timestamp":1628640000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI044170"],"award-info":[{"award-number":["AI044170"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI096528"],"award-info":[{"award-number":["AI096528"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI112445"],"award-info":[{"award-number":["AI112445"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI112949"],"award-info":[{"award-number":["AI112949"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI146432"],"award-info":[{"award-number":["AI146432"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI153069"],"award-info":[{"award-number":["AI153069"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001063","name":"Crohn's and Colitis Foundation of America","doi-asserted-by":"publisher","award":["650976"],"award-info":[{"award-number":["650976"]}],"id":[{"id":"10.13039\/100001063","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007197","name":"U.S. Public Health Service","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007197","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["bmn.com","clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Current Opinion in Microbiology"],"published-print":{"date-parts":[[2021,10]]},"DOI":"10.1016\/j.mib.2021.08.004","type":"journal-article","created":{"date-parts":[[2021,8,21]],"date-time":"2021-08-21T17:43:24Z","timestamp":1629567804000},"page":"221-230","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":45,"special_numbering":"C","title":["The longitudinal and cross-sectional heterogeneity of the intestinal microbiota"],"prefix":"10.1016","volume":"63","author":[{"given":"Brittany M","family":"Miller","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2489-5019","authenticated-orcid":false,"given":"Megan J","family":"Liou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jee-Yon","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas J","family":"B\u00e4umler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.mib.2021.08.004_bib0005","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","author":"The Human Microbiome Project Consortium","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.mib.2021.08.004_bib0010","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1016\/j.chom.2017.03.010","article-title":"The gut microbiome: connecting spatial organization to function","volume":"21","author":"Tropini","year":"2017","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.mib.2021.08.004_bib0015","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/nrmicro3552","article-title":"Gut biogeography of the bacterial microbiota","volume":"14","author":"Donaldson","year":"2016","journal-title":"Nat Rev Microbiol"},{"key":"10.1016\/j.mib.2021.08.004_bib0020","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.chom.2021.01.002","article-title":"Adherent-invasive E. coli metabolism of propanediol in Crohn\u2019s disease regulates phagocytes to drive intestinal inflammation","volume":"29","author":"Viladomiu","year":"2021","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.mib.2021.08.004_bib0025","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1126\/science.1224820","article-title":"Intestinal inflammation targets cancer-inducing activity of the microbiota","volume":"338","author":"Arthur","year":"2012","journal-title":"Science"},{"key":"10.1016\/j.mib.2021.08.004_bib0030","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature09922","article-title":"Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease","volume":"472","author":"Wang","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.mib.2021.08.004_bib0035","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1038\/nm.3444","article-title":"Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis","volume":"20","author":"Trompette","year":"2014","journal-title":"Nat Med"},{"key":"10.1016\/j.mib.2021.08.004_bib0040","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1146\/annurev-immunol-101819-024945","article-title":"The habitat filters of microbiota-nourishing immunity","volume":"39","author":"Miller","year":"2021","journal-title":"Annu Rev Immunol"},{"key":"10.1016\/j.mib.2021.08.004_bib0045","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1890\/0012-9658(2006)87[1465:ATTFHF]2.0.CO;2","article-title":"A trait-based test for habitat filtering: convex hull volume","volume":"87","author":"Cornwell","year":"2006","journal-title":"Ecology"},{"key":"10.1016\/j.mib.2021.08.004_bib0050","doi-asserted-by":"crossref","first-page":"157","DOI":"10.2307\/3235676","article-title":"Assembly and response rules - 2 goals for predictive community ecology","volume":"3","author":"Keddy","year":"1992","journal-title":"J Vegetation Sci"},{"key":"10.1016\/j.mib.2021.08.004_bib0055","doi-asserted-by":"crossref","first-page":"292","DOI":"10.3389\/fmicb.2019.00292","article-title":"A developing symbiosis: enabling cross-talk between ecologists and microbiome scientists","volume":"10","author":"Tipton","year":"2019","journal-title":"Front Microbiol"},{"key":"10.1016\/j.mib.2021.08.004_sbref0060","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s40168-020-00875-0","article-title":"Microbiome definition re-visited: old concepts and new challenges","volume":"8","author":"Berg","year":"2020","journal-title":"Microbiome"},{"key":"10.1016\/j.mib.2021.08.004_bib0065","doi-asserted-by":"crossref","first-page":"G602","DOI":"10.1152\/ajpgi.00230.2019","article-title":"Dysbiosis: from fiction to function","volume":"317","author":"Tiffany","year":"2019","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"10.1016\/j.mib.2021.08.004_bib0070","doi-asserted-by":"crossref","DOI":"10.1128\/MMBR.00027-19","article-title":"Salmonella versus the microbiome","volume":"85","author":"Rogers","year":"2021","journal-title":"Microbiol Mol Biol Rev"},{"key":"10.1016\/j.mib.2021.08.004_bib0075","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1038\/nature25973","article-title":"Environment dominates over host genetics in shaping human gut microbiota","volume":"555","author":"Rothschild","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.mib.2021.08.004_sbref0080","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1016\/j.cell.2018.10.029","article-title":"US immigration westernizes the human gut microbiome","volume":"175","author":"Vangay","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.mib.2021.08.004_bib0085","doi-asserted-by":"crossref","DOI":"10.1126\/science.aat9076","article-title":"Colonocyte metabolism shapes the gut microbiota","volume":"362","author":"Litvak","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.mib.2021.08.004_bib0090","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1038\/s41385-018-0010-y","article-title":"Healthy hosts rule within: ecological forces shaping the gut microbiota","volume":"11","author":"Byndloss","year":"2018","journal-title":"Mucosal Immunol"},{"key":"10.1016\/j.mib.2021.08.004_bib0095","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.mib.2017.07.003","article-title":"Dysbiotic proteobacteria expansion: a microbial signature of epithelial dysfunction","volume":"39","author":"Litvak","year":"2017","journal-title":"Curr Opin Microbiol"},{"key":"10.1016\/j.mib.2021.08.004_bib0100","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1038\/nrmicro2166","article-title":"Electron transfer in syntrophic communities of anaerobic bacteria and archaea","volume":"7","author":"Stams","year":"2009","journal-title":"Nat Rev Microbiol"},{"key":"10.1016\/j.mib.2021.08.004_bib0105","first-page":"86","volume":"vol 2","author":"Schmitz","year":"2006"},{"key":"10.1016\/j.mib.2021.08.004_bib0110","first-page":"299","volume":"vol 1","author":"Stahl","year":"2006"},{"key":"10.1016\/j.mib.2021.08.004_bib0115","first-page":"5","article-title":"Microorganisms and biogeochemical cycles: what can we learn from layered microbial communities?","volume":"vol 35","author":"Nealson","year":"1997"},{"key":"10.1016\/j.mib.2021.08.004_bib0120","first-page":"139","article-title":"Biological significance of short-chain fatty acid metabolism by the intestinal microbiome","volume":"17","author":"Puertollano","year":"2014","journal-title":"Curr Opin Clin Nutr Metab Care"},{"key":"10.1016\/j.mib.2021.08.004_bib0125","doi-asserted-by":"crossref","first-page":"1873","DOI":"10.1016\/j.bbapap.2008.08.012","article-title":"Acetogenesis and the wood-ljungdahl pathway of CO(2) fixation","volume":"1784","author":"Ragsdale","year":"2008","journal-title":"Biochim Biophys Acta"},{"key":"10.1016\/j.mib.2021.08.004_bib0130","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1038\/nrmicro1892","article-title":"The ecology and biotechnology of sulphate-reducing bacteria","volume":"6","author":"Muyzer","year":"2008","journal-title":"Nat Rev Microbiol"},{"key":"10.1016\/j.mib.2021.08.004_bib0135","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.scitotenv.2016.12.131","article-title":"Effect of cyclic redox oscillations on water quality in freshwater acid sulfate soil wetlands","volume":"581\u2013582","author":"Karimian","year":"2017","journal-title":"Sci Total Environ"},{"key":"10.1016\/j.mib.2021.08.004_bib0140","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1016\/j.chemosphere.2018.01.096","article-title":"Iron and sulfur cycling in acid sulfate soil wetlands under dynamic redox conditions: a review","volume":"197","author":"Karimian","year":"2018","journal-title":"Chemosphere"},{"key":"10.1016\/j.mib.2021.08.004_bib0145","first-page":"G383","article-title":"Constitutive expression of inducible nitric oxide synthase in the mouse ileal mucosa","volume":"272","author":"Hoffman","year":"1997","journal-title":"Am J Physiol"},{"key":"10.1016\/j.mib.2021.08.004_bib0150","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00960-16","article-title":"Energy taxis toward host-derived nitrate supports a Salmonella pathogenicity island 1-independent mechanism of invasion","volume":"7","author":"Rivera-Chavez","year":"2016","journal-title":"mBio"},{"key":"10.1016\/j.mib.2021.08.004_sbref0155","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1038\/mi.2017.106","article-title":"iNOS- and NOX1-dependent ROS production maintains bacterial homeostasis in the ileum of mice","volume":"11","author":"Matziouridou","year":"2018","journal-title":"Mucosal Immunol"},{"key":"10.1016\/j.mib.2021.08.004_bib0160","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/0003-9861(92)90434-X","article-title":"Bactericidal activity of peroxynitrite","volume":"298","author":"Zhu","year":"1992","journal-title":"Arch Biochem Biophys"},{"key":"10.1016\/j.mib.2021.08.004_bib0165","doi-asserted-by":"crossref","first-page":"6399","DOI":"10.1073\/pnas.92.14.6399","article-title":"Genetic and redox determinants of nitric oxide cytotoxicity in a Salmonella typhimurium model","volume":"92","author":"De Groote","year":"1995","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.mib.2021.08.004_bib0170","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1038\/nrd2222","article-title":"Peroxynitrite: biochemistry, pathophysiology and development of therapeutics","volume":"6","author":"Szabo","year":"2007","journal-title":"Nat Rev Drug Discov"},{"key":"10.1016\/j.mib.2021.08.004_bib0175","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1084\/jem.193.9.1027","article-title":"Hypoxia-inducible factor 1-dependent induction of intestinal trefoil factor protects barrier function during hypoxia","volume":"193","author":"Furuta","year":"2001","journal-title":"J Exp Med"},{"key":"10.1016\/j.mib.2021.08.004_bib0180","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1016\/j.chom.2015.03.005","article-title":"Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function","volume":"17","author":"Kelly","year":"2015","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.mib.2021.08.004_bib0185","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1126\/science.aam9949","article-title":"Microbiota-activated PPAR-g signaling inhibits dysbiotic enterobacteriaceae expansion","volume":"357","author":"Byndloss","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.mib.2021.08.004_bib0190","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1002\/j.2040-4603.2020.tb00108.x","article-title":"Intestinal absorption of bile acids in health and disease","volume":"10","author":"Ticho","year":"2019","journal-title":"Compr Physiol"},{"key":"10.1016\/j.mib.2021.08.004_sbref0195","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1016\/j.cell.2020.12.011","article-title":"Infection trains the host for microbiota-enhanced resistance to pathogens","volume":"184","author":"Stacy","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.mib.2021.08.004_bib0200","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1038\/ismej.2011.212","article-title":"The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates","volume":"6","author":"Zoetendal","year":"2012","journal-title":"ISME J"},{"key":"10.1016\/j.mib.2021.08.004_bib0205","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/nrmicro2746","article-title":"How glycan metabolism shapes the human gut microbiota","volume":"10","author":"Koropatkin","year":"2012","journal-title":"Nat Rev Microbiol"},{"key":"10.1016\/j.mib.2021.08.004_bib0210","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1111\/j.1440-1746.2010.06433.x","article-title":"Fiber, FODMAPs, flora, flatulence, and the functional bowel disorders","volume":"25","author":"Gwee","year":"2010","journal-title":"J Gastroenterol Hepatol"},{"key":"10.1016\/j.mib.2021.08.004_bib0215","doi-asserted-by":"crossref","first-page":"1035S","DOI":"10.1093\/ajcn\/69.5.1035s","article-title":"Developmental microbial ecology of the neonatal gastrointestinal tract","volume":"69","author":"Mackie","year":"1999","journal-title":"Am J Clin Nutr"},{"key":"10.1016\/j.mib.2021.08.004_bib0220","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/j.tim.2010.03.008","article-title":"Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides","volume":"18","author":"Sela","year":"2010","journal-title":"Trends Microbiol"},{"key":"10.1016\/j.mib.2021.08.004_bib0225","doi-asserted-by":"crossref","first-page":"18964","DOI":"10.1073\/pnas.0809584105","article-title":"The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome","volume":"105","author":"Sela","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.mib.2021.08.004_bib0230","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1128\/AEM.06762-11","article-title":"Bifidobacterium longum subsp. infantis ATCC 15697 alpha-fucosidases are active on fucosylated human milk oligosaccharides","volume":"78","author":"Sela","year":"2012","journal-title":"Appl Environ Microbiol"},{"key":"10.1016\/j.mib.2021.08.004_bib0235","doi-asserted-by":"crossref","first-page":"3329","DOI":"10.1099\/mic.0.043224-0","article-title":"Examination of faecal Bifidobacterium populations in breast- and formula-fed infants during the first 18 months of life","volume":"156","author":"Roger","year":"2010","journal-title":"Microbiology"},{"key":"10.1016\/j.mib.2021.08.004_bib0240","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/nrmicro3050","article-title":"The abundance and variety of carbohydrate-active enzymes in the human gut microbiota","volume":"11","author":"El Kaoutari","year":"2013","journal-title":"Nat Rev Microbiol"},{"key":"10.1016\/j.mib.2021.08.004_bib0245","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1196\/annals.1419.016","article-title":"Old acetogens, new light","volume":"1125","author":"Drake","year":"2008","journal-title":"Ann N Y Acad Sci"},{"key":"10.1016\/j.mib.2021.08.004_bib0250","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1016\/j.febslet.2012.04.043","article-title":"Pathway engineering and synthetic biology using acetogens","volume":"586","author":"Schiel-Bengelsdorf","year":"2012","journal-title":"FEBS Lett"},{"key":"10.1016\/j.mib.2021.08.004_bib0255","article-title":"Acetogen communities in the gut of herbivores and their potential role in syngas fermentation","volume":"4","author":"Yang","year":"2018","journal-title":"Ferment Basel"},{"key":"10.1016\/j.mib.2021.08.004_bib0260","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1111\/1751-7915.12400","article-title":"Electromicrobiology: realities, grand challenges, goals and predictions","volume":"9","author":"Nealson","year":"2016","journal-title":"Microb Biotechnol"},{"key":"10.1016\/j.mib.2021.08.004_sbref0265","doi-asserted-by":"crossref","first-page":"26892","DOI":"10.1073\/pnas.1915678116","article-title":"Extracellular electron transfer powers flavinylated extracellular reductases in Gram-positive bacteria","volume":"116","author":"Light","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.mib.2021.08.004_bib0270","doi-asserted-by":"crossref","first-page":"29439","DOI":"10.1021\/acsomega.0c04362","article-title":"Characterization of electrogenic gut bacteria","volume":"5","author":"Tahernia","year":"2020","journal-title":"ACS Omega"},{"key":"10.1016\/j.mib.2021.08.004_bib0275","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1111\/j.1365-2672.1988.tb01498.x","article-title":"Occurrence of sulphate-reducing bacteria in human faeces and the relationship of dissimilatory sulphate reduction to methanogenesis in the large gut","volume":"65","author":"Gibson","year":"1988","journal-title":"J Appl Bacteriol"},{"key":"10.1016\/j.mib.2021.08.004_bib0280","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1136\/gut.27.6.698","article-title":"Incidence of methanogenic bacteria in a sigmoidoscopy population: an association of methanogenic bacteria and diverticulosis","volume":"27","author":"Weaver","year":"1986","journal-title":"Gut"},{"key":"10.1016\/j.mib.2021.08.004_bib0285","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1146\/annurev.food.102308.124101","article-title":"Mechanisms of microbial hydrogen disposal in the human colon and implications for health and disease","volume":"1","author":"Nakamura","year":"2010","journal-title":"Annu Rev Food Sci Technol"},{"key":"10.1016\/j.mib.2021.08.004_bib0290","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1007\/BF00406313","article-title":"Methanobacillus omelianskii, a symbiotic association of two species of bacteria","volume":"59","author":"Bryant","year":"1967","journal-title":"Arch Mikrobiol"},{"key":"10.1016\/j.mib.2021.08.004_bib0295","first-page":"309","volume":"vol 2","author":"Schink","year":"2006"},{"key":"10.1016\/j.mib.2021.08.004_bib0300","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1111\/1574-6976.12019","article-title":"Microbial syntrophy: interaction for the common good","volume":"37","author":"Morris","year":"2013","journal-title":"FEMS Microbiol Rev"},{"key":"10.1016\/j.mib.2021.08.004_bib0305","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/0014-5793(69)80119-5","article-title":"Ferredoxin mediated hydrogen formation from NADPH in a cell-free system of Clostridium kluyveri","volume":"3","author":"Jungermann","year":"1969","journal-title":"FEBS Lett"},{"key":"10.1016\/j.mib.2021.08.004_bib0310","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1016\/0014-5793(69)80060-8","article-title":"Pyruvate synthesis from acetyl coenzyme A and carbon dioxide with NADH(2) or NADPH(2) as electron donors","volume":"2","author":"Gottschalk","year":"1969","journal-title":"FEBS Lett"},{"key":"10.1016\/j.mib.2021.08.004_bib0315","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1111\/1751-7915.12780","article-title":"Hunger and microbiology: is a low gastric acid-induced bacterial overgrowth in the small intestine a contributor to malnutrition in developing countries?","volume":"10","author":"Sarker","year":"2017","journal-title":"Microb Biotechnol"},{"key":"10.1016\/j.mib.2021.08.004_bib0320","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1097\/00004836-200001000-00017","article-title":"Intestinal motility in small bowel diverticulosis: a case report and review of the literature","volume":"30","author":"Kongara","year":"2000","journal-title":"J Clin Gastroenterol"},{"key":"10.1016\/j.mib.2021.08.004_bib0325","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1136\/bjsm.2003.006825","article-title":"Objective evaluation of small bowel and colonic transit time using pH telemetry in athletes with gastrointestinal symptoms","volume":"38","author":"Rao","year":"2004","journal-title":"Br J Sports Med"},{"key":"10.1016\/j.mib.2021.08.004_bib0330","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1136\/gut.31.8.879","article-title":"Jejunal bacterial overgrowth and intestinal permeability in children with immunodeficiency syndromes","volume":"31","author":"Pignata","year":"1990","journal-title":"Gut"},{"key":"10.1016\/j.mib.2021.08.004_bib0335","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1185\/03007999909115173","article-title":"Intestinal bacterial overgrowth during chronic pancreatitis","volume":"15","author":"Trespi","year":"1999","journal-title":"Curr Med Res Opin"},{"key":"10.1016\/j.mib.2021.08.004_bib0340","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1080\/19382014.2019.1585165","article-title":"Characterization of host defense molecules in the human pancreas","volume":"11","author":"Stenwall","year":"2019","journal-title":"Islets"},{"key":"10.1016\/j.mib.2021.08.004_bib0345","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.cmet.2017.02.007","article-title":"Orai1-mediated antimicrobial secretion from pancreatic acini shapes the gut microbiome and regulates gut innate immunity","volume":"25","author":"Ahuja","year":"2017","journal-title":"Cell Metab"},{"key":"10.1016\/j.mib.2021.08.004_bib0350","doi-asserted-by":"crossref","first-page":"2099","DOI":"10.1128\/AAC.40.9.2099","article-title":"Antimicrobial activity of human pancreatic juice and its interaction with antibiotics","volume":"40","author":"Minelli","year":"1996","journal-title":"Antimicrob Agents Chemother"},{"key":"10.1016\/j.mib.2021.08.004_bib0355","doi-asserted-by":"crossref","first-page":"2978","DOI":"10.3748\/wjg.v16.i24.2978","article-title":"Small intestinal bacterial overgrowth syndrome","volume":"16","author":"Bures","year":"2010","journal-title":"World J Gastroenterol"},{"key":"10.1016\/j.mib.2021.08.004_bib0360","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1002533","article-title":"Revised estimates for the number of human and bacteria cells in the body","volume":"14","author":"Sender","year":"2016","journal-title":"PLoS Biol"},{"key":"10.1016\/j.mib.2021.08.004_bib0365","doi-asserted-by":"crossref","DOI":"10.1038\/s41385-021-00383-w","article-title":"Host\/microbiota interactions in health and diseases-time for mucosal microbiology","author":"Daniel","year":"2021","journal-title":"Mucosal Immunol"},{"key":"10.1016\/j.mib.2021.08.004_bib0370","doi-asserted-by":"crossref","first-page":"15064","DOI":"10.1073\/pnas.0803124105","article-title":"The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria","volume":"105","author":"Johansson","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.mib.2021.08.004_bib0375","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.jcmgh.2018.09.009","article-title":"Identification of inner mucus-associated bacteria by laser capture microdissection","volume":"7","author":"Chassaing","year":"2019","journal-title":"Cell Mol Gastroenterol Hepatol"},{"key":"10.1016\/j.mib.2021.08.004_bib0380","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00116-12","article-title":"A crypt-specific core microbiota resides in the mouse colon","volume":"3","author":"Pedron","year":"2012","journal-title":"mBio"},{"key":"10.1016\/j.mib.2021.08.004_bib0385","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1007\/s00253-010-2921-8","article-title":"Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon","volume":"88","author":"Wang","year":"2010","journal-title":"Appl Microbiol Biotechnol"},{"key":"10.1016\/j.mib.2021.08.004_bib0390","doi-asserted-by":"crossref","first-page":"4720","DOI":"10.1073\/pnas.1219247110","article-title":"Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing","volume":"110","author":"Berry","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.mib.2021.08.004_bib0395","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.chom.2015.01.015","article-title":"Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque","volume":"17","author":"Yasuda","year":"2015","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.mib.2021.08.004_bib0400","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1038\/ismej.2010.161","article-title":"Spatial organization of intestinal microbiota in the mouse ascending colon","volume":"5","author":"Nava","year":"2011","journal-title":"ISME J"},{"key":"10.1016\/j.mib.2021.08.004_bib0405","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0012238","article-title":"Bacteria penetrate the inner mucus layer before inflammation in the dextran sulfate colitis model","volume":"5","author":"Johansson","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.mib.2021.08.004_bib0410","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1136\/gutjnl-2012-303207","article-title":"Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis","volume":"63","author":"Johansson","year":"2014","journal-title":"Gut"},{"key":"10.1016\/j.mib.2021.08.004_bib0415","doi-asserted-by":"crossref","first-page":"2420","DOI":"10.1038\/ajg.2010.281","article-title":"Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria","volume":"105","author":"Png","year":"2010","journal-title":"Am J Gastroenterol"},{"key":"10.1016\/j.mib.2021.08.004_bib0420","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/nature12447","article-title":"Bacterial colonization factors control specificity and stability of the gut microbiota","volume":"501","author":"Lee","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.mib.2021.08.004_bib0425","doi-asserted-by":"crossref","first-page":"1955","DOI":"10.1126\/science.1109051","article-title":"Glycan foraging in vivo by an intestine-adapted bacterial symbiont","volume":"307","author":"Sonnenburg","year":"2005","journal-title":"Science"},{"key":"10.1016\/j.mib.2021.08.004_bib0430","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1038\/nature16504","article-title":"Diet-induced extinctions in the gut microbiota compound over generations","volume":"529","author":"Sonnenburg","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.mib.2021.08.004_bib0435","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1016\/j.cell.2016.10.043","article-title":"A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility","volume":"167","author":"Desai","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.mib.2021.08.004_bib0440","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1126\/science.aaf3951","article-title":"Cospeciation of gut microbiota with hominids","volume":"353","author":"Moeller","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.mib.2021.08.004_bib0445","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1053\/j.gastro.2014.07.020","article-title":"Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota","volume":"147","author":"Albenberg","year":"2014","journal-title":"Gastroenterology"},{"key":"10.1016\/j.mib.2021.08.004_sbref0450","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1016\/j.chom.2020.09.005","article-title":"Epithelial-derived reactive oxygen species enable AppBCX-mediated aerobic respiration of Escherichia coli during intestinal inflammation","volume":"28","author":"Chanin","year":"2020","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.mib.2021.08.004_sbref0455","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.chom.2020.10.009","article-title":"Anaerobic respiration of NOX1-derived hydrogen peroxide licenses bacterial growth at the colonic surface","volume":"28","author":"Miller","year":"2020","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.mib.2021.08.004_bib0460","doi-asserted-by":"crossref","first-page":"E6922","DOI":"10.1073\/pnas.1701587114","article-title":"Escherichia coli cytochrome c peroxidase is a respiratory oxidase that enables the use of hydrogen peroxide as a terminal electron acceptor","volume":"114","author":"Khademian","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.mib.2021.08.004_bib0465","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.immuni.2019.08.003","article-title":"Microbiota-nourishing immunity: a guide to understanding our microbial self","volume":"51","author":"Litvak","year":"2019","journal-title":"Immunity"},{"key":"10.1016\/j.mib.2021.08.004_bib0470","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1093\/ibd\/izz004","article-title":"Microbiota-nourishing immunity and its relevance for ulcerative colitis","volume":"25","author":"Byndloss","year":"2019","journal-title":"Inflamm Bowel Dis"},{"key":"10.1016\/j.mib.2021.08.004_bib0475","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1111\/j.1365-2036.2009.03970.x","article-title":"Review article: small intestinal bacterial overgrowth, bile acid malabsorption and gluten intolerance as possible causes of chronic watery diarrhoea","volume":"29","author":"Fan","year":"2009","journal-title":"Aliment Pharmacol Ther"},{"key":"10.1016\/j.mib.2021.08.004_bib0480","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/j.chom.2016.03.004","article-title":"Depletion of butyrate-producing Clostridia from the gut microbiota drives an aerobic luminal expansion of Salmonella","volume":"19","author":"Rivera-Chavez","year":"2016","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.mib.2021.08.004_bib0485","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02244-19","article-title":"Increased epithelial oxygenation links colitis to an expansion of tumorigenic bacteria","volume":"10","author":"Cevallos","year":"2019","journal-title":"mBio"},{"key":"10.1016\/j.mib.2021.08.004_sbref0490","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/j.chom.2020.06.001","article-title":"High-fat diet and antibiotics cooperatively impair mitochondrial bioenergetics to trigger dysbiosis that exacerbates pre-inflammatory bowel disease","volume":"28","author":"Lee","year":"2020","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.mib.2021.08.004_bib0495","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1126\/science.1232467","article-title":"Host-derived nitrate boosts growth of E. coli in the inflamed gut","volume":"339","author":"Winter","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.mib.2021.08.004_bib0500","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00430-13","article-title":"Streptomycin-induced inflammation enhances Escherichia coli gut colonization through nitrate respiration","volume":"4","author":"Spees","year":"2013","journal-title":"mBio"},{"key":"10.1016\/j.mib.2021.08.004_bib0505","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1038\/nature25172","article-title":"Precision editing of the gut microbiota ameliorates colitis","volume":"553","author":"Zhu","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.mib.2021.08.004_bib0510","doi-asserted-by":"crossref","first-page":"2378","DOI":"10.1084\/jem.20181939","article-title":"Editing of the gut microbiota reduces carcinogenesis in mouse models of colitis-associated colorectal cancer","volume":"216","author":"Zhu","year":"2019","journal-title":"J Exp Med"},{"key":"10.1016\/j.mib.2021.08.004_bib0515","doi-asserted-by":"crossref","first-page":"1256","DOI":"10.1038\/ismej.2013.80","article-title":"Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis","volume":"7","author":"Rigottier-Gois","year":"2013","journal-title":"ISME J"},{"key":"10.1016\/j.mib.2021.08.004_bib0520","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1016\/j.tibtech.2015.06.011","article-title":"Proteobacteria: microbial signature of dysbiosis in gut microbiota","volume":"33","author":"Shin","year":"2015","journal-title":"Trends Biotechnol"},{"key":"10.1016\/j.mib.2021.08.004_bib0525","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.freeradbiomed.2016.09.022","article-title":"Oxygen as a driver of gut dysbiosis","volume":"105","author":"Rivera-Chavez","year":"2017","journal-title":"Free Radic Biol Med"},{"key":"10.1016\/j.mib.2021.08.004_bib0530","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.chom.2010.08.004","article-title":"Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis","volume":"8","author":"Garrett","year":"2010","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.mib.2021.08.004_sbref0535","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.1038\/s41385-019-0205-x","article-title":"Colitis susceptibility in mice with reactive oxygen species deficiency is mediated by mucus barrier and immune defense defects","volume":"12","author":"Aviello","year":"2019","journal-title":"Mucosal Immunol"},{"key":"10.1016\/j.mib.2021.08.004_sbref0540","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/mi.2017.74","article-title":"NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease","volume":"11","author":"Schwerd","year":"2018","journal-title":"Mucosal Immunol"},{"key":"10.1016\/j.mib.2021.08.004_bib0545","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1016\/S0016-5085(03)00271-3","article-title":"Impaired expression of peroxisome proliferator-activated receptor gamma in ulcerative colitis","volume":"124","author":"Dubuquoy","year":"2003","journal-title":"Gastroenterology"},{"key":"10.1016\/j.mib.2021.08.004_bib0550","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1016\/S0140-6736(80)91934-0","article-title":"The colonic epithelium in ulcerative colitis: an energy-deficiency disease?","volume":"2","author":"Roediger","year":"1980","journal-title":"Lancet"},{"key":"10.1016\/j.mib.2021.08.004_bib0555","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1016\/j.chom.2017.01.005","article-title":"Microbial respiration and formate oxidation as metabolic signatures of inflammation-associated dysbiosis","volume":"21","author":"Hughes","year":"2017","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.mib.2021.08.004_sbref0560","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.03227-20","article-title":"5-aminosalicylic acid ameliorates colitis and checks dysbiotic Escherichia coli expansion by activating PPAR-gamma signaling in the intestinal epithelium","volume":"12","author":"Cevallos","year":"2021","journal-title":"mBio"},{"key":"10.1016\/j.mib.2021.08.004_bib0565","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.3389\/fmicb.2018.01274","article-title":"5-Aminosalicylic acid alters the gut bacterial microbiota in patients with ulcerative colitis","volume":"9","author":"Xu","year":"2018","journal-title":"Front Microbiol"}],"container-title":["Current Opinion in Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1369527421001089?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1369527421001089?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T05:55:10Z","timestamp":1761285310000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1369527421001089"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10]]},"references-count":113,"alternative-id":["S1369527421001089"],"URL":"https:\/\/doi.org\/10.1016\/j.mib.2021.08.004","relation":{},"ISSN":["1369-5274"],"issn-type":[{"value":"1369-5274","type":"print"}],"subject":[],"published":{"date-parts":[[2021,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"The longitudinal and cross-sectional heterogeneity of the intestinal microbiota","name":"articletitle","label":"Article Title"},{"value":"Current Opinion in Microbiology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.mib.2021.08.004","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Author(s). Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}]}}