{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T12:55:24Z","timestamp":1793105724661,"version":"4.5.0"},"reference-count":75,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2021,3,1]],"date-time":"2021-03-01T00:00:00Z","timestamp":1614556800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,3,1]],"date-time":"2021-03-01T00:00:00Z","timestamp":1614556800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,3,10]],"date-time":"2022-03-10T00:00:00Z","timestamp":1646870400000},"content-version":"vor","delay-in-days":374,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,3,1]],"date-time":"2021-03-01T00:00:00Z","timestamp":1614556800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2021,3,1]],"date-time":"2021-03-01T00:00:00Z","timestamp":1614556800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2021,3,1]],"date-time":"2021-03-01T00:00:00Z","timestamp":1614556800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2021,3,1]],"date-time":"2021-03-01T00:00:00Z","timestamp":1614556800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2021,3,1]],"date-time":"2021-03-01T00:00:00Z","timestamp":1614556800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100004336","name":"Novartis","doi-asserted-by":"publisher","award":["2017091753A1"],"award-info":[{"award-number":["2017091753A1"]}],"id":[{"id":"10.13039\/100004336","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004336","name":"Novartis","doi-asserted-by":"publisher","award":["WPO2015179437A1"],"award-info":[{"award-number":["WPO2015179437A1"]}],"id":[{"id":"10.13039\/100004336","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["P2EZP3_159083"],"award-info":[{"award-number":["P2EZP3_159083"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["152527"],"award-info":[{"award-number":["152527"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006436","name":"Celgene","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006436","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000884","name":"Cancer Research Institute","doi-asserted-by":"publisher","award":["49679"],"award-info":[{"award-number":["49679"]}],"id":[{"id":"10.13039\/100000884","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI042135"],"award-info":[{"award-number":["AI042135"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P30 CA008748"],"award-info":[{"award-number":["P30 CA008748"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100002491","name":"Bristol-Myers Squibb","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100002491","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004628","name":"MedImmune","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004628","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Host &amp; Microbe"],"published-print":{"date-parts":[[2021,3]]},"DOI":"10.1016\/j.chom.2021.01.003","type":"journal-article","created":{"date-parts":[[2021,2,5]],"date-time":"2021-02-05T21:14:08Z","timestamp":1612559648000},"page":"378-393.e5","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":103,"title":["Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation"],"prefix":"10.1016","volume":"29","author":[{"given":"Simone","family":"Becattini","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew T.","family":"Sorbara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sohn G.","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric L.","family":"Littmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiwen","family":"Dong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gavin","family":"Walsh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberta","family":"Wright","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luigi","family":"Amoretti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Fontana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias M.","family":"Hohl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric G.","family":"Pamer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.chom.2021.01.003_bib1","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1080\/19490976.2018.1534514","article-title":"Modelling the role of microbial p-cresol in colorectal genotoxicity","volume":"10","author":"Al Hinai","year":"2019","journal-title":"Gut Microbes"},{"key":"10.1016\/j.chom.2021.01.003_bib2","first-page":"4135","article-title":"GPD1, which encodes glycerol-3-phosphate dehydrogenase, is essential for growth under osmotic stress in Saccharomyces cerevisiae, and its expression is regulated by the high-osmolarity glycerol response pathway","volume":"14","author":"Albertyn","year":"1994","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.chom.2021.01.003_bib74","unstructured":"Alboukadel Kassambara (2020). ggpubr: \u2018ggplot2\u2019 Based Publication Ready Plots. R package version 0.4.0. https:\/\/CRAN.R-project.org\/package=ggpubr."},{"key":"10.1016\/j.chom.2021.01.003_bib3","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.freeradbiomed.2015.04.004","article-title":"The deleterious metabolic and genotoxic effects of the bacterial metabolite p-cresol on colonic epithelial cells","volume":"85","author":"Andriamihaja","year":"2015","journal-title":"Free Radical Biol. Med."},{"key":"10.1016\/j.chom.2021.01.003_bib4","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/nature12726","article-title":"Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation","volume":"504","author":"Arpaia","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.chom.2021.01.003_bib5","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1038\/nature12331","article-title":"Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota","volume":"500","author":"Atarashi","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.chom.2021.01.003_bib6","doi-asserted-by":"crossref","first-page":"1973","DOI":"10.1084\/jem.20170495","article-title":"Commensal microbes provide first line defense against Listeria monocytogenes infection","volume":"214","author":"Becattini","year":"2017","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.chom.2021.01.003_bib7","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.cell.2014.03.011","article-title":"Role of the microbiota in immunity and inflammation","volume":"157","author":"Belkaid","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.chom.2021.01.003_bib8","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1126\/science.aau6481","article-title":"Dendritic cell\u2013derived hepcidin sequesters iron from the microbiota to promote mucosal healing","volume":"368","author":"Bessman","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.chom.2021.01.003_bib9","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1007\/s11306-014-0677-3","article-title":"Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn's disease and healthy individuals","volume":"11","author":"Bjerrum","year":"2015","journal-title":"Metabolomics"},{"key":"10.1016\/j.chom.2021.01.003_bib10","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2021.01.003_bib11","first-page":"413","article-title":"The tumor-promoting action of phenol and related compounds for mouse skin","volume":"19","author":"Boutwell","year":"1959","journal-title":"Cancer Res"},{"key":"10.1016\/j.chom.2021.01.003_bib12","doi-asserted-by":"crossref","first-page":"8365","DOI":"10.1038\/srep08365","article-title":"RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes","volume":"5","author":"Brettin","year":"2015","journal-title":"Sci. Rep."},{"key":"10.1016\/j.chom.2021.01.003_bib13","doi-asserted-by":"crossref","first-page":"16215","DOI":"10.1038\/nmicrobiol.2016.215","article-title":"Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium","volume":"2","author":"Brugiroux","year":"2016","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2021.01.003_bib14","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/nature13828","article-title":"Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile","volume":"517","author":"Buffie","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.chom.2021.01.003_bib15","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1016\/j.chom.2017.04.002","article-title":"Cooperating commensals restore colonization resistance to vancomycin-resistant Enterococcus faecium","volume":"21","author":"Caballero","year":"2017","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2021.01.003_bib16","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01442-14","article-title":"Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing","volume":"5","author":"Conway","year":"2014","journal-title":"mBio"},{"key":"10.1016\/j.chom.2021.01.003_bib17","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1038\/nature12820","article-title":"Diet rapidly and reproducibly alters the human gut microbiome","volume":"505","author":"David","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.chom.2021.01.003_bib18","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1038\/nature10228","article-title":"Control of TH17 cells occurs in the small intestine","volume":"475","author":"Esplugues","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.chom.2021.01.003_bib19","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1186\/s40425-019-0574-4","article-title":"Exploring the emerging role of the microbiome in cancer immunotherapy","volume":"7","author":"Fessler","year":"2019","journal-title":"J.\u00a0Immunother. Cancer"},{"key":"10.1016\/j.chom.2021.01.003_bib20","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.chom.2021.01.003_bib21","doi-asserted-by":"crossref","first-page":"E2329","DOI":"10.1073\/pnas.1319284111","article-title":"Relating the metatranscriptome and metagenome of the human gut","volume":"111","author":"Franzosa","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2021.01.003_bib22","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41564-018-0306-4","article-title":"Gut microbiome structure and metabolic activity in inflammatory bowel disease","volume":"4","author":"Franzosa","year":"2019","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2021.01.003_bib23","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1038\/nature12721","article-title":"Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T\u00a0cells","volume":"504","author":"Furusawa","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.chom.2021.01.003_bib24","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1016\/j.cell.2017.01.022","article-title":"Mining the human gut microbiota for immunomodulatory organisms","volume":"168","author":"Geva-Zatorsky","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.chom.2021.01.003_bib25","doi-asserted-by":"crossref","first-page":"1772","DOI":"10.1038\/s41598-019-38874-3","article-title":"Faecal bacterial and short-chain fatty acids signature in hypercholesterolemia","volume":"9","author":"Granado-Serrano","year":"2019","journal-title":"Sci Rep"},{"key":"10.1016\/j.chom.2021.01.003_bib26","first-page":"2978","article-title":"Impact of gut colonization with butyrate-producing microbiota on respiratory viral infection following allo-HCT","volume":"131","author":"Haak","year":"2018","journal-title":"Blood"},{"key":"10.1016\/j.chom.2021.01.003_bib27","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/S0065-2911(02)46002-X","article-title":"The extracytoplasmic function (ECF) sigma factors","volume":"46","author":"Helmann","year":"2002","journal-title":"Adv. Microb. Physiol."},{"key":"10.1016\/j.chom.2021.01.003_bib28","doi-asserted-by":"crossref","first-page":"12672","DOI":"10.1073\/pnas.1904099116","article-title":"Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide","volume":"116","author":"Henke","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2021.01.003_bib29","doi-asserted-by":"crossref","first-page":"1070","DOI":"10.1038\/s41591-018-0061-3","article-title":"Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women","volume":"24","author":"Hoyles","year":"2018","journal-title":"Nat. Med."},{"key":"10.1016\/j.chom.2021.01.003_bib30","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/j.immuni.2011.01.020","article-title":"Th17 cells express interleukin-10 receptor and are controlled by Foxp3(-) and Foxp3+ regulatory CD4+ T\u00a0cells in an interleukin-10-dependent manner","volume":"34","author":"Huber","year":"2011","journal-title":"Immunity"},{"key":"10.1016\/j.chom.2021.01.003_bib31","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.chom.2021.01.003_bib32","doi-asserted-by":"crossref","first-page":"2389","DOI":"10.1038\/ismej.2016.40","article-title":"Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling","volume":"10","author":"Ilott","year":"2016","journal-title":"ISME J."},{"key":"10.1016\/j.chom.2021.01.003_bib33","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/j.cell.2009.09.033","article-title":"Induction of intestinal Th17 cells by segmented filamentous bacteria","volume":"139","author":"Ivanov","year":"2009","journal-title":"Cell"},{"key":"10.1016\/j.chom.2021.01.003_bib34","doi-asserted-by":"crossref","first-page":"e6386","DOI":"10.1371\/journal.pone.0006386","article-title":"Metabolomics reveals metabolic biomarkers of Crohn's disease","volume":"4","author":"Jansson","year":"2009","journal-title":"PLoS One"},{"key":"10.1016\/j.chom.2021.01.003_bib35","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1038\/s41586-019-1501-z","article-title":"Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus","volume":"572","author":"Kim","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.chom.2021.01.003_bib36","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/j.immuni.2011.12.011","article-title":"Interleukin 23 production by intestinal CD103(+)CD11b(+) dendritic cells in response to bacterial flagellin enhances mucosal innate immune defense","volume":"36","author":"Kinnebrew","year":"2012","journal-title":"Immunity"},{"key":"10.1016\/j.chom.2021.01.003_bib37","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1126\/science.aac4812","article-title":"Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples","volume":"349","author":"Korem","year":"2015","journal-title":"Science"},{"key":"10.1016\/j.chom.2021.01.003_bib38","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.chom.2021.01.003_bib39","doi-asserted-by":"crossref","first-page":"e1002995","DOI":"10.1371\/journal.ppat.1002995","article-title":"Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice","volume":"8","author":"Lawley","year":"2012","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.chom.2021.01.003_bib40","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.3389\/fimmu.2019.01420","article-title":"Complex bacterial consortia reprogram the colitogenic activity of Enterococcus faecalis in a gnotobiotic mouse model of chronic, immune-mediated colitis","volume":"10","author":"Lengfelder","year":"2019","journal-title":"Front. Immunol."},{"key":"10.1016\/j.chom.2021.01.003_bib41","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.chom.2021.01.003_bib42","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases","volume":"569","author":"Lloyd-Price","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.chom.2021.01.003_bib43","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.chom.2021.01.003_bib44","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1021\/pr060470d","article-title":"Rapid and noninvasive metabonomic characterization of inflammatory bowel disease","volume":"6","author":"Marchesi","year":"2007","journal-title":"J.\u00a0Proteome Res."},{"key":"10.1016\/j.chom.2021.01.003_bib45","doi-asserted-by":"crossref","first-page":"e140","DOI":"10.1093\/nar\/gkt444","article-title":"Computational analysis of bacterial RNA-Seq data","volume":"41","author":"McClure","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2021.01.003_bib46","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1136\/gut.51.2.155","article-title":"Defining the roles of perforin, Fas\/FasL, and tumour necrosis factor alpha in T\u00a0cell induced mucosal damage in the mouse intestine","volume":"51","author":"Merger","year":"2002","journal-title":"Gut"},{"key":"10.1016\/j.chom.2021.01.003_bib47","doi-asserted-by":"crossref","first-page":"R79","DOI":"10.1186\/gb-2012-13-9-r79","article-title":"Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment","volume":"13","author":"Morgan","year":"2012","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2021.01.003_bib48","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00036-12","article-title":"The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss","volume":"3","author":"Morris","year":"2012","journal-title":"mBio"},{"key":"10.1016\/j.chom.2021.01.003_bib49","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1172\/JCI0215695","article-title":"T cell activation causes diarrhea by increasing intestinal permeability and inhibiting epithelial Na+\/K+-ATPase","volume":"110","author":"Musch","year":"2002","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.chom.2021.01.003_bib50","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1016\/j.chom.2020.04.013","article-title":"Import of aspartate and malate by DcuABC drives H2\/fumarate respiration to promote initial salmonella gut-lumen colonization in mice","volume":"27","author":"Nguyen","year":"2020","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2021.01.003_bib51","doi-asserted-by":"crossref","first-page":"e1004911","DOI":"10.1371\/journal.ppat.1004911","article-title":"Surface-associated lipoproteins link Enterococcus faecalis virulence to colitogenic activity in IL-10-deficient mice independent of their expression levels","volume":"11","author":"Ocvirk","year":"2015","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.chom.2021.01.003_bib52","doi-asserted-by":"crossref","first-page":"1842","DOI":"10.1053\/j.gastro.2011.06.064","article-title":"Chronic intestinal inflammation induces stress-response genes in commensal Escherichia coli","volume":"141","author":"Patwa","year":"2011","journal-title":"Gastroenterology"},{"key":"10.1016\/j.chom.2021.01.003_bib53","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/nature13823","article-title":"Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness","volume":"514","author":"Pickard","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.chom.2021.01.003_bib75","unstructured":"R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https:\/\/www.R-project.org\/."},{"key":"10.1016\/j.chom.2021.01.003_bib54","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.cell.2004.07.002","article-title":"Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis","volume":"118","author":"Rakoff-Nahoum","year":"2004","journal-title":"Cell"},{"key":"10.1016\/j.chom.2021.01.003_bib55","doi-asserted-by":"crossref","first-page":"3786","DOI":"10.1128\/IAI.00647-12","article-title":"Suppression of Clostridium difficile in the gastrointestinal tracts of germfree mice inoculated with a murine isolate from the family Lachnospiraceae","volume":"80","author":"Reeves","year":"2012","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2021.01.003_bib56","doi-asserted-by":"crossref","first-page":"6032","DOI":"10.1128\/JB.186.18.6032-6041.2004","article-title":"Escherichia coli glutamate- and arginine-dependent acid resistance systems increase internal pH and reverse transmembrane potential","volume":"186","author":"Richard","year":"2004","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.chom.2021.01.003_bib57","doi-asserted-by":"crossref","first-page":"5143","DOI":"10.1128\/AEM.00482-06","article-title":"Production of a heterologous nonheme catalase by Lactobacillus casei: an efficient tool for removal of H2O2 and protection of Lactobacillus bulgaricus from oxidative stress in milk","volume":"72","author":"Rochat","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.chom.2021.01.003_bib58","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.3945\/ajcn.110.002188","article-title":"High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health","volume":"93","author":"Russell","year":"2011","journal-title":"Am. J. Clin. Nutr."},{"key":"10.1016\/j.chom.2021.01.003_bib59","doi-asserted-by":"crossref","first-page":"e01202","DOI":"10.7554\/eLife.01202","article-title":"Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis","volume":"2","author":"Scher","year":"2013","journal-title":"eLife"},{"key":"10.1016\/j.chom.2021.01.003_bib60","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/s41564-017-0089-z","article-title":"Dynamics of metatranscription in the inflammatory bowel disease gut microbiome","volume":"3","author":"Schirmer","year":"2018","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2021.01.003_bib61","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1038\/ismej.2013.223","article-title":"Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery","volume":"8","author":"Schwab","year":"2014","journal-title":"ISME J."},{"key":"10.1016\/j.chom.2021.01.003_bib62","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1126\/science.1241165","article-title":"The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis","volume":"341","author":"Smith","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.chom.2021.01.003_bib63","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1084\/jem.20181639","article-title":"Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification","volume":"216","author":"Sorbara","year":"2019","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.chom.2021.01.003_bib64","doi-asserted-by":"crossref","first-page":"9285","DOI":"10.1074\/jbc.RA119.008439","article-title":"Oleate hydratase from Staphylococcus aureus protects against palmitoleic acid, the major antimicrobial fatty acid produced by mammalian skin","volume":"294","author":"Subramanian","year":"2019","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.chom.2021.01.003_bib65","doi-asserted-by":"crossref","first-page":"D553","DOI":"10.1093\/nar\/gkt1274","article-title":"RefSeq microbial genomes database: new representation and annotation strategy","volume":"42","author":"Tatusova","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.chom.2021.01.003_bib66","doi-asserted-by":"crossref","first-page":"2526","DOI":"10.1073\/pnas.1716888115","article-title":"Metabolic division of labor in microbial systems","volume":"115","author":"Tsoi","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2021.01.003_bib67","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.3389\/fmicb.2016.01144","article-title":"Gut microbiota profiling: metabolomics based approach to unravel compounds affecting human health","volume":"7","author":"Vernocchi","year":"2016","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.chom.2021.01.003_bib68","doi-asserted-by":"crossref","first-page":"2069","DOI":"10.1097\/MIB.0b013e31829a91f6","article-title":"Analysis of volatile organic compounds of bacterial origin in chronic gastrointestinal diseases","volume":"19","author":"Walton","year":"2013","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.chom.2021.01.003_bib69","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkw1017","article-title":"Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center","volume":"45","author":"Wattam","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2021.01.003_bib70","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1002\/jobm.200610263","article-title":"Isolation of a FAD-GPDH gene encoding a mitochondrial FAD-dependent glycerol-3-phosphate dehydrogenase from Dunaliella salina","volume":"47","author":"Yang","year":"2007","journal-title":"J.\u00a0Basic Microbiol."},{"key":"10.1016\/j.chom.2021.01.003_bib71","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"Omics"},{"key":"10.1016\/j.chom.2021.01.003_bib72","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1101\/gr.200602","article-title":"Computational identification of operons in microbial genomes","volume":"12","author":"Zheng","year":"2002","journal-title":"Genome Res."},{"key":"10.1016\/j.chom.2021.01.003_bib73","doi-asserted-by":"crossref","first-page":"G599","DOI":"10.1152\/ajpgi.00063.2004","article-title":"IL-10 modulates intestinal damage and epithelial cell apoptosis in T\u00a0cell-mediated enteropathy","volume":"287","author":"Zhou","year":"2004","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."}],"container-title":["Cell Host &amp; Microbe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312821000330?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312821000330?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T08:08:40Z","timestamp":1778832520000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1931312821000330"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,3]]},"references-count":75,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2021,3]]}},"alternative-id":["S1931312821000330"],"URL":"https:\/\/doi.org\/10.1016\/j.chom.2021.01.003","relation":{},"ISSN":["1931-3128"],"issn-type":[{"value":"1931-3128","type":"print"}],"subject":[],"published":{"date-parts":[[2021,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation","name":"articletitle","label":"Article Title"},{"value":"Cell Host & Microbe","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.chom.2021.01.003","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 Elsevier Inc.","name":"copyright","label":"Copyright"}]}}