{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T02:15:50Z","timestamp":1791944150925,"version":"4.3.4"},"reference-count":210,"publisher":"Elsevier BV","issue":"13","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["1R01DK134692"],"award-info":[{"award-number":["1R01DK134692"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013140","name":"Colorectal Cancer Alliance","doi-asserted-by":"publisher","award":["10065978"],"award-info":[{"award-number":["10065978"]}],"id":[{"id":"10.13039\/100013140","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM150625"],"award-info":[{"award-number":["R35GM150625"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001033","name":"Jane Coffin Childs Memorial Fund for Medical Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001033","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020194","name":"Vanderbilt Digestive Diseases Research Center, Vanderbilt University Medical Center","doi-asserted-by":"publisher","award":["DK058404"],"award-info":[{"award-number":["DK058404"]}],"id":[{"id":"10.13039\/100020194","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001368","name":"V Foundation for Cancer Research","doi-asserted-by":"publisher","award":["V2022-032"],"award-info":[{"award-number":["V2022-032"]}],"id":[{"id":"10.13039\/100001368","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001229","name":"G. Harold and Leila Y. Mathers Charitable Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001229","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007208","name":"Vanderbilt Cancer Center","doi-asserted-by":"publisher","award":["P30 CA068485"],"award-info":[{"award-number":["P30 CA068485"]}],"id":[{"id":"10.13039\/100007208","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011671","name":"G Harold and Leila Y Mathers Foundation","doi-asserted-by":"publisher","award":["MF-2207-03128"],"award-info":[{"award-number":["MF-2207-03128"]}],"id":[{"id":"10.13039\/100011671","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013677","name":"University of California Davis West Coast Metabolomics Center","doi-asserted-by":"publisher","award":["1U2C-DK119889"],"award-info":[{"award-number":["1U2C-DK119889"]}],"id":[{"id":"10.13039\/100013677","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["1R35GM147470"],"award-info":[{"award-number":["1R35GM147470"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"National Institute of Allergy and Infectious Diseases Division of Intramural Research","doi-asserted-by":"publisher","award":["F31AI178950"],"award-info":[{"award-number":["F31AI178950"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell"],"published-print":{"date-parts":[[2026,6]]},"DOI":"10.1016\/j.cell.2026.04.012","type":"journal-article","created":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T14:50:22Z","timestamp":1777560622000},"page":"3968-3990.e38","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":8,"title":["An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut"],"prefix":"10.1016","volume":"189","author":[{"given":"Luisella","family":"Spiga","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan T.","family":"Fansler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifan","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Grote","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madison","family":"Langford-Butler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asia K.","family":"Miller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxwell","family":"Neal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Owen F.","family":"Hale","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deepanshu","family":"Singla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Wade","family":"Calcutt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abigail E.","family":"Rose","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madeline M.","family":"Bresson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra C.","family":"Schrimpe-Rutledge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brittany","family":"Berdy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simona G.","family":"Codreanu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary Kay","family":"Washington","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin P.","family":"Bratton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stacy D.","family":"Sherrod","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John A.","family":"McLean","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karsten","family":"Zengler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cynthia L.","family":"Sears","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megan G.","family":"Behringer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Gnirke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lili","family":"Tao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Livny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danyvid","family":"Olivares-Villag\u00f3mez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashlee M.","family":"Earl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3771-0842","authenticated-orcid":false,"given":"Wenhan","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.cell.2026.04.012_bib1","doi-asserted-by":"crossref","DOI":"10.1016\/j.soh.2024.100075","article-title":"Global burden of enteric infections related foodborne diseases, 1990\u20132021: findings from the Global Burden of Disease Study 2021","volume":"3","author":"Li","year":"2024","journal-title":"Sci. One Health"},{"key":"10.1016\/j.cell.2026.04.012_bib2","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1038\/s41579-023-00973-4","article-title":"The microbial landscape of colorectal cancer","volume":"22","author":"White","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib3","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1038\/s41575-019-0209-8","article-title":"Gut microbiota in colorectal cancer: mechanisms of action and clinical applications","volume":"16","author":"Wong","year":"2019","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"10.1016\/j.cell.2026.04.012_bib4","doi-asserted-by":"crossref","first-page":"1510","DOI":"10.1002\/ijc.30583","article-title":"Concordant and discordant familial cancer: Familial risks, proportions and population impact","volume":"140","author":"Frank","year":"2017","journal-title":"Int. J. Cancer"},{"key":"10.1016\/j.cell.2026.04.012_bib5","doi-asserted-by":"crossref","first-page":"e116","DOI":"10.1016\/S1470-2045(21)00588-X","article-title":"A comprehensive framework for early-onset colorectal cancer research","volume":"23","author":"Eng","year":"2022","journal-title":"Lancet Oncol."},{"key":"10.1016\/j.cell.2026.04.012_bib6","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.tim.2020.01.001","article-title":"Microbiome in Colorectal Cancer: How to Get from Meta-omics to Mechanism?","volume":"28","author":"Ternes","year":"2020","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib7","doi-asserted-by":"crossref","first-page":"1873","DOI":"10.1158\/2159-8290.CD-21-1273","article-title":"Human Colon Cancer-Derived Clostridioides difficile Strains Drive Colonic Tumorigenesis in Mice","volume":"12","author":"Drewes","year":"2022","journal-title":"Cancer Discov."},{"key":"10.1016\/j.cell.2026.04.012_bib8","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1128\/CMR.00053-08","article-title":"Enterotoxigenic Bacteroides fragilis: a rogue among symbiotes","volume":"22","author":"Sears","year":"2009","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.cell.2026.04.012_bib9","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/s41586-020-2080-8","article-title":"Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli","volume":"580","author":"Pleguezuelos-Manzano","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.cell.2026.04.012_bib10","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1086\/591130","article-title":"Association of enterotoxigenic Bacteroides fragilis infection with inflammatory diarrhea","volume":"47","author":"Sears","year":"2008","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.cell.2026.04.012_bib11","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1186\/s12885-019-6115-1","article-title":"The association between fecal enterotoxigenic B. fragilis with colorectal cancer","volume":"19","author":"Haghi","year":"2019","journal-title":"BMC Cancer"},{"key":"10.1016\/j.cell.2026.04.012_bib12","doi-asserted-by":"crossref","first-page":"449","DOI":"10.3389\/fcimb.2019.00449","article-title":"Enterotoxigenic Bacteroides fragilis: A Possible Etiological Candidate for Bacterially-Induced Colorectal Precancerous and Cancerous Lesions","volume":"9","author":"Zamani","year":"2019","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib13","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1093\/cid\/ciu787","article-title":"The Bacteroides fragilis toxin gene is prevalent in the colon mucosa of colorectal cancer patients","volume":"60","author":"Boleij","year":"2015","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.cell.2026.04.012_bib14","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1111\/j.1469-0691.2006.01494.x","article-title":"A possible role of Bacteroides fragilis enterotoxin in the aetiology of colorectal cancer","volume":"12","author":"Toprak","year":"2006","journal-title":"Clin. Microbiol. Infect."},{"key":"10.1016\/j.cell.2026.04.012_bib15","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1126\/science.aah3648","article-title":"Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria","volume":"359","author":"Dejea","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.04.012_bib16","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1186\/s12879-014-0733-7","article-title":"Escherichia coli strains of phylogenetic group B2 and D and bacteriocin production are associated with advanced colorectal neoplasia","volume":"14","author":"Kohoutova","year":"2014","journal-title":"BMC Infect. Dis."},{"key":"10.1016\/j.cell.2026.04.012_bib17","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1126\/science.1127059","article-title":"Escherichia coli induces DNA double-strand breaks in eukaryotic cells","volume":"313","author":"Nougayr\u00e8de","year":"2006","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.04.012_bib18","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1136\/gutjnl-2013-304739","article-title":"Colonic mucosa-associated diffusely adherent afaC+ Escherichia coli expressing lpfA and pks are increased in inflammatory bowel disease and colon cancer","volume":"63","author":"Prorok-Hamon","year":"2014","journal-title":"Gut"},{"key":"10.1016\/j.cell.2026.04.012_bib19","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1186\/s12885-021-09110-x","article-title":"High frequency of enterotoxigenic Bacteroides fragilis and Enterococcus faecalis in the paraffin-embedded tissues of Iranian colorectal cancer patients","volume":"21","author":"Khodaverdi","year":"2021","journal-title":"BMC Cancer"},{"key":"10.1016\/j.cell.2026.04.012_bib20","doi-asserted-by":"crossref","first-page":"80794","DOI":"10.18632\/oncotarget.13094","article-title":"Association of oncogenic bacteria with colorectal cancer in South China","volume":"7","author":"Zhou","year":"2016","journal-title":"Oncotarget"},{"key":"10.1016\/j.cell.2026.04.012_bib21","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.anaerobe.2004.10.004","article-title":"Diarrhea caused by enterotoxigenic Bacteroides fragilis in children less than 5 years of age in Hanoi, Vietnam","volume":"11","author":"Vu Nguyen","year":"2005","journal-title":"Anaerobe"},{"key":"10.1016\/j.cell.2026.04.012_bib22","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/j.ijid.2005.05.009","article-title":"Etiology and epidemiology of diarrhea in children in Hanoi, Vietnam","volume":"10","author":"Vu Nguyen","year":"2006","journal-title":"Int. J. Infect Dis."},{"key":"10.1016\/j.cell.2026.04.012_bib23","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1016\/j.anaerobe.2005.06.001","article-title":"Prevalence of enterotoxigenic Bacteroides fragilis in patients with diarrhea: a controlled study","volume":"11","author":"Durmaz","year":"2005","journal-title":"Anaerobe"},{"key":"10.1016\/j.cell.2026.04.012_bib24","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1128\/IAI.00814-08","article-title":"Induction of persistent colitis by a human commensal, enterotoxigenic Bacteroides fragilis, in wild-type C57BL\/6 mice","volume":"77","author":"Rhee","year":"2009","journal-title":"Infect. Immun."},{"key":"10.1016\/j.cell.2026.04.012_bib25","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.cell.2026.04.012_bib26","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1038\/nm.2015","article-title":"A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses","volume":"15","author":"Wu","year":"2009","journal-title":"Nat. Med."},{"key":"10.1016\/j.cell.2026.04.012_bib27","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.cell.2026.04.012_bib28","doi-asserted-by":"crossref","first-page":"2060","DOI":"10.3390\/cancers13092060","article-title":"Colibactin-Producing Escherichia coli Induce the Formation of Invasive Carcinomas in a Chronic Inflammation-Associated Mouse Model","volume":"13","author":"Salesse","year":"2021","journal-title":"Cancers (Basel)"},{"key":"10.1016\/j.cell.2026.04.012_bib29","doi-asserted-by":"crossref","first-page":"1932","DOI":"10.1136\/gutjnl-2013-305257","article-title":"Bacterial genotoxin colibactin promotes colon tumour growth by inducing a senescence-associated secretory phenotype","volume":"63","author":"Cougnoux","year":"2014","journal-title":"Gut"},{"key":"10.1016\/j.cell.2026.04.012_bib30","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.chom.2018.01.007","article-title":"Bacteroides fragilis Toxin Coordinates a Pro-carcinogenic Inflammatory Cascade via Targeting of Colonic Epithelial Cells","volume":"23","author":"Chung","year":"2018","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cell.2026.04.012_bib31","doi-asserted-by":"crossref","first-page":"5382","DOI":"10.1128\/IAI.00060-06","article-title":"The Bacteroides fragilis toxin binds to a specific intestinal epithelial cell receptor","volume":"74","author":"Wu","year":"2006","journal-title":"Infect. Immun."},{"key":"10.1016\/j.cell.2026.04.012_bib32","doi-asserted-by":"crossref","first-page":"5595","DOI":"10.1128\/IAI.00135-06","article-title":"The C-terminal region of Bacteroides fragilis toxin is essential to its biological activity","volume":"74","author":"Sears","year":"2006","journal-title":"Infect. Immun."},{"key":"10.1016\/j.cell.2026.04.012_bib33","doi-asserted-by":"crossref","first-page":"1944","DOI":"10.1242\/jcs.03455","article-title":"Bacteroides fragilis toxin stimulates intestinal epithelial cell shedding and gamma-secretase-dependent E-cadherin cleavage","volume":"120","author":"Wu","year":"2007","journal-title":"J. Cell Sci."},{"key":"10.1016\/j.cell.2026.04.012_bib34","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/s41564-023-01559-9","article-title":"Bacteroides fragilis toxin expression enables lamina propria niche acquisition in the developing mouse gut","volume":"9","author":"Hill","year":"2024","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib35","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/j.chom.2017.08.007","article-title":"A Two-Component System Regulates Bacteroides fragilis Toxin to Maintain Intestinal Homeostasis and Prevent Lethal Disease","volume":"22","author":"Hecht","year":"2017","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cell.2026.04.012_bib36","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.cell.2026.04.012_bib37","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1016\/S0016-5085(82)80339-9","article-title":"Utilization of nutrients by isolated epithelial cells of the rat colon","volume":"83","author":"Roediger","year":"1982","journal-title":"Gastroenterology"},{"key":"10.1016\/j.cell.2026.04.012_bib38","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.cell.2026.04.012_bib39","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.cell.2026.04.012_bib40","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1146\/annurev-micro-102215-095316","article-title":"The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology","volume":"71","author":"Porter","year":"2017","journal-title":"Annu. Rev. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib41","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41385-018-0053-0","article-title":"Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them","volume":"12","author":"Sorbara","year":"2019","journal-title":"Mucosal Immunol."},{"key":"10.1016\/j.cell.2026.04.012_bib42","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41586-021-03502-6","article-title":"C. difficile exploits a host metabolite produced during toxin-mediated disease","volume":"593","author":"Pruss","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.cell.2026.04.012_bib43","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1126\/science.aag3042","article-title":"Virulence factors enhance Citrobacter rodentium expansion through aerobic respiration","volume":"353","author":"Lopez","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.04.012_bib44","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1038\/s41586-019-1453-3","article-title":"Cholera toxin promotes pathogen acquisition of host-derived nutrients","volume":"572","author":"Rivera-Ch\u00e1vez","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.cell.2026.04.012_bib45","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1038\/s41579-021-00583-y","article-title":"When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence","volume":"19","author":"Lu","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib46","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1146\/annurev.mi.38.100184.001453","article-title":"Bacteroides of the human lower intestinal tract","volume":"38","author":"Salyers","year":"1984","journal-title":"Annu. Rev. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib47","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1016\/j.chom.2009.05.010","article-title":"Importance of glycans to the host-bacteroides mutualism in the mammalian intestine","volume":"5","author":"Comstock","year":"2009","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cell.2026.04.012_bib48","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.chom.2011.10.002","article-title":"Eating for two: how metabolism establishes interspecies interactions in the gut","volume":"10","author":"Fischbach","year":"2011","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cell.2026.04.012_bib49","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1098\/rstb.1995.0152","article-title":"The Leeuwenhoek Lecture, 1995. Adaptation to life without oxygen","volume":"350","author":"Guest","year":"1995","journal-title":"Philos. Trans. R. Soc. Lond., B Biol. Sci."},{"key":"10.1016\/j.cell.2026.04.012_bib50","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.cell.2026.04.012_bib51","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1016\/j.chom.2024.05.011","article-title":"Nutrient acquisition strategies by gut microbes","volume":"32","author":"Muramatsu","year":"2024","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cell.2026.04.012_bib52","doi-asserted-by":"crossref","first-page":"17480","DOI":"10.1073\/pnas.1107857108","article-title":"Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota","volume":"108","author":"Thiennimitr","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.04.012_bib53","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/nature09415","article-title":"Gut inflammation provides a respiratory electron acceptor for Salmonella","volume":"467","author":"Winter","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.cell.2026.04.012_bib54","doi-asserted-by":"crossref","first-page":"1774","DOI":"10.1016\/j.chom.2024.07.025","article-title":"Salmonella re-engineers the intestinal environment to break colonization resistance in the presence of a compositionally intact microbiota","volume":"32","author":"Rogers","year":"2024","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cell.2026.04.012_bib55","doi-asserted-by":"crossref","first-page":"e00027-19","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.cell.2026.04.012_bib56","doi-asserted-by":"crossref","first-page":"4991","DOI":"10.1128\/JB.00875-13","article-title":"Probing bacterial metabolism during infection using high-resolution transcriptomics","volume":"195","author":"Jorth","year":"2013","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.cell.2026.04.012_bib57","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1038\/s41564-024-01642-9","article-title":"An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity","volume":"9","author":"Ryan","year":"2024","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib58","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1006033","article-title":"Resolving host-pathogen interactions by dual RNA-seq","volume":"13","author":"Westermann","year":"2017","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.cell.2026.04.012_bib59","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1515\/hsz-2020-0230","article-title":"An RNA-centric view on gut Bacteroidetes","volume":"402","author":"Ryan","year":"2020","journal-title":"Biol. Chem."},{"key":"10.1016\/j.cell.2026.04.012_bib60","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-55633-6","article-title":"Hybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis","volume":"9","author":"Betin","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.cell.2026.04.012_bib61","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1038\/s41564-020-0683-3","article-title":"Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice","volume":"5","author":"Donaldson","year":"2020","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib62","doi-asserted-by":"crossref","DOI":"10.1038\/nmicrobiol.2017.67","article-title":"Convergent evolution of a modified, acetate-driven TCA cycle in bacteria","volume":"2","author":"Kwong","year":"2017","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib63","doi-asserted-by":"crossref","first-page":"3664","DOI":"10.1016\/S0021-9258(18)97196-6","article-title":"Regulation of alpha-ketoglutarate dehydrogenase formation in Escherichia coli","volume":"240","author":"Amarasingham","year":"1965","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.cell.2026.04.012_bib64","doi-asserted-by":"crossref","DOI":"10.1128\/ecosalplus.3.5.2","article-title":"Tricarboxylic Acid Cycle and Glyoxylate Bypass","volume":"1","author":"Cronan","year":"2005","journal-title":"EcoSal Plus"},{"key":"10.1016\/j.cell.2026.04.012_bib65","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1038\/nature02285","article-title":"The strict anaerobe Bacteroides fragilis grows in and benefits from nanomolar concentrations of oxygen","volume":"427","author":"Baughn","year":"2004","journal-title":"Nature"},{"key":"10.1016\/j.cell.2026.04.012_bib66","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.cell.2026.04.012_bib67","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/S0065-2911(08)60123-X","article-title":"Microbial anaerobic respiration","volume":"31","author":"Moodie","year":"1990","journal-title":"Adv. Microbiol. Physiol."},{"key":"10.1016\/j.cell.2026.04.012_bib68","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.tim.2022.08.006","article-title":"Something old, something new, something borrowed, something blue: the anaerobic microbial ancestry of aerobic respiration","volume":"31","author":"Glass","year":"2023","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib69","doi-asserted-by":"crossref","DOI":"10.1093\/femsre\/fuac006","article-title":"How low can they go? Aerobic respiration by microorganisms under apparent anoxia","volume":"46","author":"Berg","year":"2022","journal-title":"FEMS Microbiol. Rev."},{"key":"10.1016\/j.cell.2026.04.012_bib70","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1046\/j.1365-2958.1999.01337.x","article-title":"Characterization of the Batl (Bacteroides aerotolerance) operon in Bacteroides fragilis: isolation of a B. fragilis mutant with reduced aerotolerance and impaired growth in in vivo model systems","volume":"32","author":"Tang","year":"1999","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib71","doi-asserted-by":"crossref","DOI":"10.1128\/jb.00389-22","article-title":"Bacteroides fragilis Maintains Concurrent Capability for Anaerobic and Nanaerobic Respiration","volume":"205","author":"Butler","year":"2023","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.cell.2026.04.012_bib72","doi-asserted-by":"crossref","first-page":"24484","DOI":"10.1073\/pnas.2009556117","article-title":"Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts","volume":"117","author":"Garc\u00eda-Bayona","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.04.012_bib73","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/0923-2508(94)90092-2","article-title":"Aerobic-anaerobic gene regulation in Escherichia coli: control by the ArcAB and Fnr regulons","volume":"145","author":"Gunsalus","year":"1994","journal-title":"Res. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib74","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-018-23446-8","article-title":"Author Correction: Lactate oxidation facilitates growth of Mycobacterium tuberculosis in human macrophages","volume":"8","author":"Billig","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.cell.2026.04.012_bib75","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.chom.2017.11.006","article-title":"Dysbiosis-Associated Change in Host Metabolism Generates Lactate to Support Salmonella Growth","volume":"23","author":"Gillis","year":"2018","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cell.2026.04.012_bib76","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/s41564-023-01560-2","article-title":"Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration","volume":"9","author":"Little","year":"2024","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib77","doi-asserted-by":"crossref","first-page":"7924","DOI":"10.1073\/pnas.89.17.7924","article-title":"Multicellular oxidant defense in unicellular organisms","volume":"89","author":"Ma","year":"1992","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.04.012_bib78","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1128\/IAI.66.4.1735-1739.1998","article-title":"Molecular characterization of the fragilysin pathogenicity islet of enterotoxigenic Bacteroides fragilis","volume":"66","author":"Moncrief","year":"1998","journal-title":"Infect. Immun."},{"key":"10.1016\/j.cell.2026.04.012_bib79","doi-asserted-by":"crossref","first-page":"6623","DOI":"10.1128\/JB.181.21.6623-6633.1999","article-title":"Molecular evolution of the pathogenicity island of enterotoxigenic Bacteroides fragilis strains","volume":"181","author":"Franco","year":"1999","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.cell.2026.04.012_bib80","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1016\/j.cell.2017.03.045","article-title":"Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut","volume":"169","author":"Lim","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.cell.2026.04.012_bib81","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1046\/j.1365-2958.2002.03077.x","article-title":"Modulation of bft expression by the Bacteroides fragilis pathogenicity island and its flanking region","volume":"45","author":"Franco","year":"2002","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib82","doi-asserted-by":"crossref","first-page":"4945","DOI":"10.1128\/IAI.67.9.4945-4949.1999","article-title":"Identification of a third metalloprotease toxin gene in extraintestinal isolates of Bacteroides fragilis","volume":"67","author":"Chung","year":"1999","journal-title":"Infect. Immun."},{"key":"10.1016\/j.cell.2026.04.012_bib83","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1128\/iai.65.3.1007-1013.1997","article-title":"Cloning and characterization of the Bacteroides fragilis metalloprotease toxin gene","volume":"65","author":"Franco","year":"1997","journal-title":"Infect. Immun."},{"key":"10.1016\/j.cell.2026.04.012_bib84","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1111\/j.1574-6968.2000.tb08892.x","article-title":"A new subtype of the metalloprotease toxin gene and the incidence of the three bft subtypes among Bacteroides fragilis isolates in Japan","volume":"182","author":"Kato","year":"2000","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.cell.2026.04.012_bib85","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1111\/j.1574-6968.1997.tb10205.x","article-title":"Cloning and characterization of the gene for the metalloprotease enterotoxin of Bacteroides fragilis","volume":"146","author":"Kling","year":"1997","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.cell.2026.04.012_bib86","doi-asserted-by":"crossref","first-page":"12153","DOI":"10.1073\/pnas.1203796109","article-title":"Inactivation of a single gene enables microaerobic growth of the obligate anaerobe Bacteroides fragilis","volume":"109","author":"Meehan","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.04.012_bib87","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1126\/science.aad9948","article-title":"Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease","volume":"352","author":"Chu","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.04.012_bib88","doi-asserted-by":"crossref","DOI":"10.1016\/j.abb.2023.109667","article-title":"Lactate oxidation is linked to energy conservation and to oxygen detoxification via a putative terminal cytochrome oxidase in Methanosarcina acetivorans","volume":"743","author":"Feregrino-Mondrag\u00f3n","year":"2023","journal-title":"Arch. Biochem. Biophys."},{"key":"10.1016\/j.cell.2026.04.012_bib89","doi-asserted-by":"crossref","first-page":"e00773-18","DOI":"10.1128\/IAI.00773-18","article-title":"Host-Derived Metabolites Modulate Transcription of Salmonella Genes Involved in l-Lactate Utilization during Gut Colonization","volume":"87","author":"Gillis","year":"2019","journal-title":"Infect. Immun."},{"key":"10.1016\/j.cell.2026.04.012_bib90","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1016\/j.tim.2014.05.008","article-title":"Microbial lactate utilization: enzymes, pathogenesis, and regulation","volume":"22","author":"Jiang","year":"2014","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib91","doi-asserted-by":"crossref","first-page":"6640","DOI":"10.1073\/pnas.120163297","article-title":"One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products","volume":"97","author":"Datsenko","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.04.012_bib92","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrmicro787","article-title":"The regulation of bacterial transcription initiation","volume":"2","author":"Browning","year":"2004","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib93","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1093\/nar\/gkw007","article-title":"Transcription-coupled DNA supercoiling dictates the chromosomal arrangement of bacterial genes","volume":"44","author":"Sobetzko","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.04.012_bib94","doi-asserted-by":"crossref","first-page":"11383","DOI":"10.1093\/nar\/gku828","article-title":"Chromosome position effects on gene expression in Escherichia coli K-12","volume":"42","author":"Bryant","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.04.012_bib95","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.65993","article-title":"Local genetic context shapes the function of a gene regulatory network","volume":"10","author":"Nagy-Staron","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.cell.2026.04.012_bib96","doi-asserted-by":"crossref","first-page":"2558","DOI":"10.1128\/JB.00142-15","article-title":"Critical Components of the Conjugation Machinery of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis","volume":"197","author":"Leonetti","year":"2015","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.cell.2026.04.012_bib97","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1128\/JB.00860-09","article-title":"Polar positioning of a conjugation protein from the integrative and conjugative element ICEBs1 of Bacillus subtilis","volume":"192","author":"Berkmen","year":"2010","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.cell.2026.04.012_bib98","doi-asserted-by":"crossref","first-page":"4942","DOI":"10.1128\/JB.00298-06","article-title":"Functional identification of conjugation and replication regions of the tetracycline resistance plasmid pCW3 from Clostridium perfringens","volume":"188","author":"Bannam","year":"2006","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.cell.2026.04.012_bib99","doi-asserted-by":"crossref","first-page":"14979","DOI":"10.1073\/pnas.95.25.14979","article-title":"Bacteroides fragilis enterotoxin cleaves the zonula adherens protein, E-cadherin","volume":"95","author":"Wu","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.04.012_bib100","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1053\/gast.2003.50047","article-title":"Bacteroides fragilis enterotoxin induces c-Myc expression and cellular proliferation","volume":"124","author":"Wu","year":"2003","journal-title":"Gastroenterology"},{"key":"10.1016\/j.cell.2026.04.012_bib101","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/s41385-022-00514-x","article-title":"Intestinal epithelial cell metabolism at the interface of microbial dysbiosis and tissue injury","volume":"15","author":"Rath","year":"2022","journal-title":"Mucosal Immunol."},{"key":"10.1016\/j.cell.2026.04.012_bib102","doi-asserted-by":"crossref","first-page":"G1","DOI":"10.1152\/ajpgi.00052.2015","article-title":"A bioassay to measure energy metabolism in mouse colonic crypts, organoids, and sorted stem cells","volume":"309","author":"Fan","year":"2015","journal-title":"Am. J. Physiol., Gastrointest. Liver Physiol."},{"key":"10.1016\/j.cell.2026.04.012_bib103","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.immuni.2024.04.022","article-title":"Metabolic coordination between skin epithelium and type 17 immunity sustains chronic skin inflammation","volume":"57","author":"Subudhi","year":"2024","journal-title":"Immunity"},{"key":"10.1016\/j.cell.2026.04.012_bib104","doi-asserted-by":"crossref","DOI":"10.1126\/science.abg9302","article-title":"Interleukin-17 governs hypoxic adaptation of injured epithelium","volume":"377","author":"Konieczny","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.04.012_bib105","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/s41586-019-1785-z","article-title":"Bile acid metabolites control TH17 and Treg cell differentiation","volume":"576","author":"Hang","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.cell.2026.04.012_bib106","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s40170-018-0182-7","article-title":"Inflammation-induced DNA methylation of DNA polymerase gamma alters the metabolic profile of colon tumors","volume":"6","author":"Maiuri","year":"2018","journal-title":"Cancer Metab."},{"key":"10.1016\/j.cell.2026.04.012_bib107","doi-asserted-by":"crossref","first-page":"4166","DOI":"10.1172\/JCI72334","article-title":"Bacteroides fragilis subverts mucosal biology: from symbiont to colon carcinogenesis","volume":"124","author":"Sears","year":"2014","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.cell.2026.04.012_bib108","doi-asserted-by":"crossref","first-page":"823","DOI":"10.18632\/aging.100232","article-title":"A STAT3-mediated metabolic switch is involved in tumour transformation and STAT3 addiction","volume":"2","author":"Demaria","year":"2010","journal-title":"Aging (Albany, NY)"},{"key":"10.1016\/j.cell.2026.04.012_bib109","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.tibs.2015.12.001","article-title":"The Warburg Effect: How Does it Benefit Cancer Cells?","volume":"41","author":"Liberti","year":"2016","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.cell.2026.04.012_bib110","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1126\/science.aam9949","article-title":"Microbiota-activated PPAR-gamma signaling inhibits dysbiotic Enterobacteriaceae expansion","volume":"357","author":"Byndloss","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.04.012_bib111","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1016\/j.cmet.2020.11.007","article-title":"SCENITH: A Flow Cytometry-Based Method to Functionally Profile Energy Metabolism with Single-Cell Resolution","volume":"32","author":"Arg\u00fcello","year":"2020","journal-title":"Cell Metab."},{"key":"10.1016\/j.cell.2026.04.012_bib112","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1038\/s41596-018-0100-z","article-title":"Cell-type-specific quantification of protein synthesis in vivo","volume":"14","author":"Hidalgo San Jose","year":"2019","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.cell.2026.04.012_bib113","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-Ch\u00e1vez","year":"2016","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cell.2026.04.012_bib114","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1016\/j.chom.2018.03.013","article-title":"Dysbiosis-Associated Change in Host Metabolism Generates Lactate to Support Salmonella Growth","volume":"23","author":"Gillis","year":"2018","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cell.2026.04.012_bib115","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1186\/s40168-022-01389-7","article-title":"Colonocyte-derived lactate promotes E. coli fitness in the context of inflammation-associated gut microbiota dysbiosis","volume":"10","author":"Taylor","year":"2022","journal-title":"Microbiome"},{"key":"10.1016\/j.cell.2026.04.012_bib116","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1111\/mmi.14516","article-title":"Do reactive oxygen species or does oxygen itself confer obligate anaerobiosis? The case of Bacteroides thetaiotaomicron","volume":"114","author":"Khademian","year":"2020","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib117","doi-asserted-by":"crossref","first-page":"1562","DOI":"10.1046\/j.1365-2958.2001.02343.x","article-title":"How does oxygen inhibit central metabolism in the obligate anaerobe Bacteroides thetaiotaomicron","volume":"39","author":"Pan","year":"2001","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.cell.2026.04.012_bib118","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1667\/0033-7587(2001)155[0015:EOODIR]2.0.CO;2","article-title":"Estimation of oxygen distribution in RIF-1 tumors by diffusion model-based interpretation of pimonidazole hypoxia and eppendorf measurements","volume":"155","author":"Pogue","year":"2001","journal-title":"Radiat. Res."},{"key":"10.1016\/j.cell.2026.04.012_bib119","doi-asserted-by":"crossref","DOI":"10.1080\/2162402X.2019.1665975","article-title":"IFN\u03b2-producing CX3CR1+ macrophages promote T-regulatory cell expansion and tumor growth in the APCmin\/+ \/ Bacteroides fragilis colon cancer model","volume":"8","author":"Gu","year":"2019","journal-title":"Oncoimmunology"},{"key":"10.1016\/j.cell.2026.04.012_bib120","doi-asserted-by":"crossref","first-page":"4560","DOI":"10.3390\/ijms20184560","article-title":"Zerumbone Suppresses Enterotoxigenic Bacteroides fragilis Infection-Induced Colonic Inflammation through Inhibition of NF-\u03ba\u0392","volume":"20","author":"Hwang","year":"2019","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.cell.2026.04.012_bib121","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1158\/2159-8290.CD-15-0447","article-title":"Regulatory T-cell Response to Enterotoxigenic Bacteroides fragilis Colonization Triggers IL17-Dependent Colon Carcinogenesis","volume":"5","author":"Geis","year":"2015","journal-title":"Cancer Discov."},{"key":"10.1016\/j.cell.2026.04.012_bib122","doi-asserted-by":"crossref","first-page":"3","DOI":"10.4161\/cc.9.1.10352","article-title":"Enterotoxigenic Bacteroides fragilis (ETBF)-mediated colitis in Min (Apc+\/-) mice: a human commensal-based murine model of colon carcinogenesis","volume":"9","author":"Housseau","year":"2010","journal-title":"Cell Cycle (Georget. Tex.)"},{"key":"10.1016\/j.cell.2026.04.012_bib123","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.chembiol.2025.12.009","article-title":"Mechanistic diversity of Bacteroides fragilis toxins and neutralization with single domain antibody","volume":"33","author":"Guo","year":"2026","journal-title":"Cell Chem. Biol."},{"key":"10.1016\/j.cell.2026.04.012_bib124","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.micpath.2015.05.003","article-title":"Recombinant fragilysin isoforms cause E-cadherin cleavage of intact cells and do not cleave isolated E-cadherin","volume":"83\u201384","author":"Kharlampieva","year":"2015","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.cell.2026.04.012_bib125","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1046\/j.1365-2125.1998.00639.x","article-title":"Results of single and repeat dose studies of the oral matrix metalloproteinase inhibitor marimastat in healthy male volunteers","volume":"45","author":"Millar","year":"1998","journal-title":"Br. J. Clin. Pharmacol."},{"key":"10.1016\/j.cell.2026.04.012_bib126","doi-asserted-by":"crossref","first-page":"4013","DOI":"10.1242\/jcs.203687","article-title":"E-cadherin cleavage by MT2-MMP regulates apical junctional signaling and epithelial homeostasis in the intestine","volume":"130","author":"G\u00f3mez-Escudero","year":"2017","journal-title":"J. Cell Sci."},{"key":"10.1016\/j.cell.2026.04.012_bib127","doi-asserted-by":"crossref","first-page":"1475","DOI":"10.1002\/ibd.20265","article-title":"Enterotoxigenic bacteroides fragilis: a potential instigator of colitis","volume":"13","author":"Rabizadeh","year":"2007","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.cell.2026.04.012_bib128","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/j.cmet.2011.02.018","article-title":"The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon","volume":"13","author":"Donohoe","year":"2011","journal-title":"Cell Metab."},{"key":"10.1016\/j.cell.2026.04.012_bib129","doi-asserted-by":"crossref","first-page":"550","DOI":"10.3892\/mmr.2021.12189","article-title":"Porcupine inhibitor LGK-974 inhibits Wnt\/\u03b2-catenin signaling and modifies tumor-associated macrophages resulting in inhibition of the malignant behaviors of non-small cell lung cancer cells","volume":"24","author":"Tang","year":"2021","journal-title":"Mol. Med. Rep."},{"key":"10.1016\/j.cell.2026.04.012_bib130","doi-asserted-by":"crossref","first-page":"20224","DOI":"10.1073\/pnas.1314239110","article-title":"Targeting Wnt-driven cancer through the inhibition of Porcupine by LGK974","volume":"110","author":"Liu","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.04.012_bib131","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1084\/jem.20090207","article-title":"IL-17 can promote tumor growth through an IL-6-Stat3 signaling pathway","volume":"206","author":"Wang","year":"2009","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.cell.2026.04.012_bib132","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1158\/0008-5472.CAN-15-0749","article-title":"Redundant Innate and Adaptive Sources of IL17 Production Drive Colon Tumorigenesis","volume":"76","author":"Housseau","year":"2016","journal-title":"Cancer Res."},{"key":"10.1016\/j.cell.2026.04.012_bib133","doi-asserted-by":"crossref","first-page":"1955","DOI":"10.1194\/jlr.R900010-JLR200","article-title":"Bile acids: regulation of synthesis","volume":"50","author":"Chiang","year":"2009","journal-title":"J. Lipid Res."},{"key":"10.1016\/j.cell.2026.04.012_bib134","doi-asserted-by":"crossref","DOI":"10.1080\/19490976.2023.2172671","article-title":"Bile acids as modulators of gut microbiota composition and function","volume":"15","author":"Larabi","year":"2023","journal-title":"Gut Microbes"},{"key":"10.1016\/j.cell.2026.04.012_bib135","doi-asserted-by":"crossref","first-page":"E7","DOI":"10.1038\/s41586-020-2030-5","article-title":"Author Correction: Bile acid metabolites control TH17 and Treg cell differentiation","volume":"579","author":"Hang","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.cell.2026.04.012_bib136","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41586-022-04480-z","article-title":"Human gut bacteria produce \u039717-modulating bile acid metabolites","volume":"603","author":"Paik","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.cell.2026.04.012_bib137","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.immuni.2009.06.020","article-title":"Interleukin-17-producing gammadelta T cells selectively expand in response to pathogen products and environmental signals","volume":"31","author":"Martin","year":"2009","journal-title":"Immunity"},{"key":"10.1016\/j.cell.2026.04.012_bib138","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1016\/j.immuni.2014.06.017","article-title":"Transcription factor T-bet regulates intraepithelial lymphocyte functional maturation","volume":"41","author":"Reis","year":"2014","journal-title":"Immunity"},{"key":"10.1016\/j.cell.2026.04.012_bib139","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1038\/mi.2016.53","article-title":"The myeloid immune signature of enterotoxigenic Bacteroides fragilis-induced murine colon tumorigenesis","volume":"10","author":"Thiele Orberg","year":"2017","journal-title":"Mucosal Immunol."},{"key":"10.1016\/j.cell.2026.04.012_bib140","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1093\/infdis\/jiw069","article-title":"Reduction of Murine Colon Tumorigenesis Driven by Enterotoxigenic Bacteroides fragilis Using Cefoxitin Treatment","volume":"214","author":"DeStefano Shields","year":"2016","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.cell.2026.04.012_bib141","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1093\/infdis\/jis771","article-title":"Successful therapy of visceral leishmaniasis with curdlan involves T-helper 17 cytokines","volume":"207","author":"Ghosh","year":"2013","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.cell.2026.04.012_bib142","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0013418","article-title":"Human dendritic cells activated via dectin-1 are efficient at priming Th17, cytotoxic CD8 T and B cell responses","volume":"5","author":"Agrawal","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.cell.2026.04.012_bib143","doi-asserted-by":"crossref","DOI":"10.4049\/jimmunol.182.Supp.47.12","article-title":"Curdlan induces Th17 polarization via Jagged1 activation in human dendritic cells (47.12)","volume":"182","author":"Matsushita","year":"2009","journal-title":"J. Immunol."},{"key":"10.1016\/j.cell.2026.04.012_bib144","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms12368","article-title":"Dectin-1-activated dendritic cells trigger potent antitumour immunity through the induction of Th9 cells","volume":"7","author":"Zhao","year":"2016","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cell.2026.04.012_bib145","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1016\/j.chom.2019.03.003","article-title":"Colitis-Induced Th17 Cells Increase the Risk for Severe Subsequent Clostridium difficile Infection","volume":"25","author":"Saleh","year":"2019","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cell.2026.04.012_bib146","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1186\/s12967-021-02943-x","article-title":"Lactobacillus paracasei R3 protects against dextran sulfate sodium (DSS)-induced colitis in mice via regulating Th17\/Treg cell balance","volume":"19","author":"Huang","year":"2021","journal-title":"J. Transl. Med."},{"key":"10.1016\/j.cell.2026.04.012_bib147","doi-asserted-by":"crossref","DOI":"10.14814\/phy2.14733","article-title":"Sexually dimorphic response of mice to the Western-style diet caused by deficiency of fatty acid binding protein 6 (Fabp6)","volume":"9","author":"Habib","year":"2021","journal-title":"Physiol. Rep."},{"key":"10.1016\/j.cell.2026.04.012_bib148","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/s40168-021-01101-1","article-title":"Review: microbial transformations of human bile acids","volume":"9","author":"Guzior","year":"2021","journal-title":"Microbiome"},{"key":"10.1016\/j.cell.2026.04.012_bib149","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1194\/jlr.R054114","article-title":"Intestinal transport and metabolism of bile acids","volume":"56","author":"Dawson","year":"2015","journal-title":"J. Lipid Res."},{"key":"10.1016\/j.cell.2026.04.012_bib150","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1194\/jlr.R900012-JLR200","article-title":"Bile acid transporters","volume":"50","author":"Dawson","year":"2009","journal-title":"J. Lipid Res."},{"key":"10.1016\/j.cell.2026.04.012_bib151","doi-asserted-by":"crossref","first-page":"1614","DOI":"10.1194\/jlr.M200469-JLR200","article-title":"Inhibition of ileal bile acid transport and reduced atherosclerosis in apoE-\/- mice by SC-435","volume":"44","author":"Bhat","year":"2003","journal-title":"J. Lipid Res."},{"key":"10.1016\/j.cell.2026.04.012_bib152","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1097\/MIB.0000000000000019","article-title":"Stat3 activation in murine colitis induced by enterotoxigenic Bacteroides fragilis","volume":"20","author":"Wick","year":"2014","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.cell.2026.04.012_bib153","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1080\/19490976.2017.1290758","article-title":"The Bacteroides fragilis pathogenicity island links virulence and strain competition","volume":"8","author":"Casterline","year":"2017","journal-title":"Gut Microbes"},{"key":"10.1016\/j.cell.2026.04.012_bib154","doi-asserted-by":"crossref","DOI":"10.1080\/19490976.2024.2361493","article-title":"Disruption of intestinal oxygen balance in acute colitis alters the gut microbiome","volume":"16","author":"Zong","year":"2024","journal-title":"Gut Microbes"},{"key":"10.1016\/j.cell.2026.04.012_bib155","doi-asserted-by":"crossref","DOI":"10.1126\/science.abp9960","article-title":"The microbiome and gut homeostasis","volume":"377","author":"Lee","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.04.012_bib156","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.cell.2026.04.012_bib157","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1016\/j.jcmgh.2021.02.007","article-title":"Regulation of Intestinal Barrier Function by Microbial Metabolites","volume":"11","author":"Ghosh","year":"2021","journal-title":"Cell. Mol. Gastroenterol. Hepatol."},{"key":"10.1016\/j.cell.2026.04.012_bib158","doi-asserted-by":"crossref","first-page":"G378","DOI":"10.1152\/ajpgi.00435.2016","article-title":"The bile acids, deoxycholic acid and ursodeoxycholic acid, regulate colonic epithelial wound healing","volume":"314","author":"Mroz","year":"2018","journal-title":"Am. J. Physiol., Gastrointest. Liver Physiol."},{"key":"10.1016\/j.cell.2026.04.012_bib159","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1111\/jgh.15676","article-title":"Deoxycholic acid delays the wound healing of colonic epithelial cells via transmembrane G-protein-coupled receptor 5","volume":"37","author":"Azuma","year":"2022","journal-title":"J. Gastroenterol. Hepatol."},{"key":"10.1016\/j.cell.2026.04.012_bib160","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1016\/j.cell.2010.05.005","article-title":"Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations","volume":"141","author":"Sonnenburg","year":"2010","journal-title":"Cell"},{"key":"10.1016\/j.cell.2026.04.012_bib161","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1093\/clinids\/23.2.269","article-title":"Detection of toxin production by Bacteroides fragilis: assay development and screening of extraintestinal clinical isolates","volume":"23","author":"Mundy","year":"1996","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.cell.2026.04.012_bib162","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1099\/00207713-26-2-230","volume":"26","author":"Cato","year":"1976","journal-title":"Int. J. Syst. Bacteriol."},{"key":"10.1016\/j.cell.2026.04.012_bib163","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1038\/nbt1183-784","article-title":"A Broad Host Range Mobilization System for In Vivo Genetic Engineering: Transposon Mutagenesis in Gram Negative Bacteria","volume":"1","author":"Simon","year":"1983","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cell.2026.04.012_bib164","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1126\/science.adj9504","article-title":"A ubiquitous mobile genetic element changes the antagonistic weaponry of a human gut symbiont","volume":"386","author":"Sheahan","year":"2024","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.04.012_bib165","doi-asserted-by":"crossref","first-page":"14919","DOI":"10.1073\/pnas.0404172101","article-title":"Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation","volume":"101","author":"Kuwahara","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.04.012_bib166","doi-asserted-by":"crossref","first-page":"e00577-18","DOI":"10.1128\/JB.00577-18","article-title":"Identification of a Fifth Antibacterial Toxin Produced by a Single Bacteroides fragilis Strain","volume":"201","author":"Shumaker","year":"2019","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.cell.2026.04.012_bib167","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.cub.2013.10.077","article-title":"An ecological network of polysaccharide utilization among human intestinal symbionts","volume":"24","author":"Rakoff-Nahoum","year":"2014","journal-title":"Curr. Biol."},{"key":"10.1016\/j.cell.2026.04.012_bib168","doi-asserted-by":"crossref","first-page":"e01902-17","DOI":"10.1128\/mBio.01902-17","article-title":"Gut Symbiont Bacteroides fragilis Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism","volume":"8","author":"Chatzidaki-Livanis","year":"2017","journal-title":"mBio"},{"key":"10.1016\/j.cell.2026.04.012_bib169","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1016\/j.str.2008.03.017","article-title":"Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices","volume":"16","author":"Koropatkin","year":"2008","journal-title":"Structure"},{"key":"10.1016\/j.cell.2026.04.012_bib170","first-page":"33","article-title":"The use of real-time reverse transcriptase PCR for the quantification of cytokine gene expression","volume":"14","author":"Overbergh","year":"2003","journal-title":"J. Biomol. Tech."},{"key":"10.1016\/j.cell.2026.04.012_bib171","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.1128\/IAI.01691-07","article-title":"T cells help to amplify inflammatory responses induced by Salmonella enterica serotype Typhimurium in the intestinal mucosa","volume":"76","author":"Godinez","year":"2008","journal-title":"Infect. Immun."},{"key":"10.1016\/j.cell.2026.04.012_bib172","article-title":"Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data","volume":"2","author":"Akhmedov","year":"2020","journal-title":"NAR Genom. Bioinform."},{"key":"10.1016\/j.cell.2026.04.012_bib173","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2026.04.012_bib174","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.cell.2026.04.012_bib175","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol. Evol."},{"key":"10.1016\/j.cell.2026.04.012_bib176","doi-asserted-by":"crossref","first-page":"W388","DOI":"10.1093\/nar\/gkab382","article-title":"MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights","volume":"49","author":"Pang","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.04.012_bib177","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1038\/s41597-024-03571-y","article-title":"Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets","volume":"11","author":"O\u2019Leary","year":"2024","journal-title":"Sci. Data"},{"key":"10.1016\/j.cell.2026.04.012_bib178","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.cell.2026.04.012_bib179","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cell.2026.04.012_bib180","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.04.012_bib181","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.1099\/mic.0.26948-0","article-title":"Transcriptional regulation of the Bacteroides fragilis ferritin gene (ftnA) by redox stress","volume":"150","author":"Rocha","year":"2004","journal-title":"Microbiology (Reading)"},{"key":"10.1016\/j.cell.2026.04.012_bib182","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1006\/mpat.1996.0018","article-title":"A comparison of the haemagglutinating and enzymic activities of Bacteroides fragilis whole cells and outer membrane vesicles","volume":"20","author":"Patrick","year":"1996","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.cell.2026.04.012_bib183","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1016\/j.chom.2023.08.018","article-title":"Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection","volume":"31","author":"Spiga","year":"2023","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.cell.2026.04.012_bib184","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/nmeth.3313","article-title":"Simultaneous generation of many RNA-seq libraries in a single reaction","volume":"12","author":"Shishkin","year":"2015","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2026.04.012_bib185","doi-asserted-by":"crossref","first-page":"1858","DOI":"10.1038\/s41591-019-0650-9","article-title":"Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination","volume":"25","author":"Bhattacharyya","year":"2019","journal-title":"Nat. Med."},{"key":"10.1016\/j.cell.2026.04.012_bib186","doi-asserted-by":"crossref","first-page":"892","DOI":"10.2144\/01304pf02","article-title":"Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction","volume":"30","author":"Zhu","year":"2001","journal-title":"BioTechniques"},{"key":"10.1016\/j.cell.2026.04.012_bib187","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cell.2026.04.012_bib188","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2026.04.012_bib189","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cell.2026.04.012_bib190","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkr995","article-title":"GenomeView: a next-generation genome browser","volume":"40","author":"Abeel","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.04.012_bib191","doi-asserted-by":"crossref","first-page":"4666","DOI":"10.1074\/jbc.M109.086678","article-title":"Cerebrospinal fluid steroidomics: are bioactive bile acids present in brain?","volume":"285","author":"Ogundare","year":"2010","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.cell.2026.04.012_bib192","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.3390\/cells10051194","article-title":"Metabolomic Analysis Evidences That Uterine Epithelial Cells Enhance Blastocyst Development in a Microfluidic Device","volume":"10","author":"Mancini","year":"2021","journal-title":"Cells"},{"key":"10.1016\/j.cell.2026.04.012_bib193","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1186\/s12974-016-0760-y","article-title":"Metabolic consequences of inflammatory disruption of the blood-brain barrier in an organ-on-chip model of the human neurovascular unit","volume":"13","author":"Brown","year":"2016","journal-title":"J. Neuroinflamm."},{"key":"10.1016\/j.cell.2026.04.012_bib194","doi-asserted-by":"crossref","DOI":"10.1063\/1.5016433","article-title":"Engineered microfluidic bioreactor for examining the three-dimensional breast tumor microenvironment","volume":"12","author":"Rogers","year":"2018","journal-title":"Biomicrofluidics"},{"key":"10.1016\/j.cell.2026.04.012_bib195","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.60191","article-title":"MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with host cell factor-1","volume":"10","author":"Popay","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.cell.2026.04.012_bib196","doi-asserted-by":"crossref","DOI":"10.1016\/j.dib.2020.105811","article-title":"Data highlighting phenotypic diversity of urine-associated Escherichia coli isolates","volume":"31","author":"Eberly","year":"2020","journal-title":"Data Brief"},{"key":"10.1016\/j.cell.2026.04.012_bib197","doi-asserted-by":"crossref","first-page":"1897","DOI":"10.1007\/s13361-016-1469-y","article-title":"Untargeted Metabolomics Strategies-Challenges and Emerging Directions","volume":"27","author":"Schrimpe-Rutledge","year":"2016","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"10.1016\/j.cell.2026.04.012_bib198","doi-asserted-by":"crossref","first-page":"D801","DOI":"10.1093\/nar\/gks1065","article-title":"HMDB 3.0--The Human Metabolome Database in 2013","volume":"41","author":"Wishart","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.04.012_bib199","doi-asserted-by":"crossref","first-page":"e86","DOI":"10.1002\/cpbi.86","article-title":"Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis","volume":"68","author":"Chong","year":"2019","journal-title":"Curr. Protoc. Bioinform."},{"key":"10.1016\/j.cell.2026.04.012_bib200","doi-asserted-by":"crossref","first-page":"2194","DOI":"10.1093\/bioinformatics\/btr381","article-title":"UCHIME improves sensitivity and speed of chimera detection","volume":"27","author":"Edgar","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cell.2026.04.012_bib201","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cell.2026.04.012_bib202","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1038\/nprot.2009.203","article-title":"A protocol for generating a high-quality genome-scale metabolic reconstruction","volume":"5","author":"Thiele","year":"2010","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.cell.2026.04.012_bib203","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/s41596-018-0098-2","article-title":"Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0","volume":"14","author":"Heirendt","year":"2019","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.cell.2026.04.012_bib204","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1011594","article-title":"Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R","volume":"19","author":"Neal","year":"2023","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.cell.2026.04.012_bib205","doi-asserted-by":"crossref","first-page":"D515","DOI":"10.1093\/nar\/gkv1049","article-title":"BiGG Models: A platform for integrating, standardizing and sharing genome-scale models","volume":"44","author":"King","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.04.012_bib206","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1038\/nbt.3956","article-title":"iML1515, a knowledgebase that computes Escherichia coli traits","volume":"35","author":"Monk","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cell.2026.04.012_bib207","doi-asserted-by":"crossref","first-page":"20338","DOI":"10.1073\/pnas.1307797110","article-title":"Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments","volume":"110","author":"Monk","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.04.012_bib208","doi-asserted-by":"crossref","first-page":"1710","DOI":"10.1128\/JB.01218-10","article-title":"An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228","volume":"193","author":"Liao","year":"2011","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.cell.2026.04.012_bib209","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1007764","article-title":"StanDep: Capturing transcriptomic variability improves context-specific metabolic models","volume":"16","author":"Joshi","year":"2020","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.cell.2026.04.012_bib210","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1038\/msb.2010.47","article-title":"Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models","volume":"6","author":"Lewis","year":"2010","journal-title":"Mol. Syst. Biol."}],"container-title":["Cell"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0092867426004010?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0092867426004010?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T06:11:58Z","timestamp":1785910318000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0092867426004010"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6]]},"references-count":210,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2026,6]]}},"alternative-id":["S0092867426004010"],"URL":"https:\/\/doi.org\/10.1016\/j.cell.2026.04.012","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.05.31.657111","asserted-by":"object"}]},"ISSN":["0092-8674"],"issn-type":[{"value":"0092-8674","type":"print"}],"subject":[],"published":{"date-parts":[[2026,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut","name":"articletitle","label":"Article Title"},{"value":"Cell","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cell.2026.04.012","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}