{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T03:26:40Z","timestamp":1792294000004,"version":"4.4.0"},"reference-count":65,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,2,28]],"date-time":"2025-02-28T00:00:00Z","timestamp":1740700800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,2,28]],"date-time":"2025-02-28T00:00:00Z","timestamp":1740700800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100000833","name":"Rosetrees Trust","doi-asserted-by":"publisher","award":["A2194"],"award-info":[{"award-number":["A2194"]}],"id":[{"id":"10.13039\/501100000833","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000833","name":"Rosetrees Trust","doi-asserted-by":"publisher","award":["PGS22\/100116"],"award-info":[{"award-number":["PGS22\/100116"]}],"id":[{"id":"10.13039\/501100000833","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["098051"],"award-info":[{"award-number":["098051"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["206245\/Z\/17\/Z"],"award-info":[{"award-number":["206245\/Z\/17\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microbiome"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Promoting resistance to enteric pathogen infection is a core function of the gut microbiota; however, many of the specific host\u2013commensal interactions that mediate this protection remain uncharacterised. To address this knowledge gap, we monocolonised germ-free mice with mouse-derived commensal microbes to screen for microbiota-induced resistance to\n                      <jats:italic>Salmonella<\/jats:italic>\n                      Typhimurium infection.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We identified\n                      <jats:italic>Enterocloster clostridioformis<\/jats:italic>\n                      as a protective species against\n                      <jats:italic>S.<\/jats:italic>\n                      Typhimurium infection.\n                      <jats:italic>E. clostridioformis<\/jats:italic>\n                      selectively upregulates resistin-like molecule \u03b2 and cell cycle pathway expression at the level of caecal epithelial cells and increases T-regulatory cells in the underlying mucosal immune system, potentially contributing to reduced infection-induced pathology.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>We highlight novel mechanisms of host\u2013microbe interactions that can mediate microbiota-induced resistance to acute salmonellosis. In the backdrop of increasing antibiotic resistance, this study identifies novel potential avenues for further research into protective host responses against enteric infections and could lead to new therapeutic approaches.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s40168-025-02050-9","type":"journal-article","created":{"date-parts":[[2025,2,28]],"date-time":"2025-02-28T03:22:08Z","timestamp":1740712928000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function"],"prefix":"10.1186","volume":"13","author":[{"given":"Benjamin S.","family":"Beresford-Jones","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Satoshi","family":"Suyama","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Clare","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amelia","family":"Soderholm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wangmingyu","family":"Xia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Puspendu","family":"Sardar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junhee","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine","family":"Harcourt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trevor D.","family":"Lawley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Virginia A.","family":"Pedicord","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,2,28]]},"reference":[{"issue":"6","key":"2050_CR1","doi-asserted-by":"publisher","first-page":"1421","DOI":"10.1080\/21645515.2018.1504717","volume":"15","author":"R Balasubramanian","year":"2019","unstructured":"Balasubramanian R, Im J, Lee JS, Jeon HJ, Mogeni OD, Kim JH, Rakotozandrindrainy R, Baker S, Marks F. The global burden and epidemiology of invasive non-typhoidal Salmonella infections. Hum Vaccin Immunother. 2019;15(6):1421\u20136.","journal-title":"Hum Vaccin Immunother"},{"key":"2050_CR2","doi-asserted-by":"crossref","unstructured":"Majowicz SE, Musto J, Scallan E, Angulo FJ, Kirk M, O\u2019Brien SJ, Jones TF, Fazil A, Hoekstra RM, International Collaboration on Enteric Disease 'Burden of Illness S. The global burden of nontyphoidal Salmonella gastroenteritis. Clin Infect Dis. 2010;50(6):882\u20139.","DOI":"10.1086\/650733"},{"issue":"12","key":"2050_CR3","doi-asserted-by":"publisher","first-page":"e1001921","DOI":"10.1371\/journal.pmed.1001921","volume":"12","author":"MD Kirk","year":"2015","unstructured":"Kirk MD, Pires SM, Black RE, Caipo M, Crump JA, Devleesschauwer B, Dopfer D, Fazil A, Fischer-Walker CL, Hald T, et al. World Health Organization estimates of the global and regional disease burden of 22 foodborne bacterial, protozoal, and viral diseases, 2010: a data synthesis. PLoS Med. 2015;12(12):e1001921.","journal-title":"PLoS Med"},{"issue":"10","key":"2050_CR4","doi-asserted-by":"publisher","first-page":"2070","DOI":"10.14202\/vetworld.2020.2070-2084","volume":"13","author":"RE Castro-Vargas","year":"2020","unstructured":"Castro-Vargas RE, Herrera-Sanchez MP, Rodriguez-Hernandez R, Rondon-Barragan IS. Antibiotic resistance in Salmonella spp. isolated from poultry: a global overview. Vet World. 2020;13(10):2070\u201384.","journal-title":"Vet World"},{"issue":"8","key":"2050_CR5","doi-asserted-by":"publisher","first-page":"1364","DOI":"10.4315\/0362-028X.JFP-18-552","volume":"82","author":"R Tasmin","year":"2019","unstructured":"Tasmin R, Gulig PA, Parveen S. Detection of virulence plasmid-encoded genes in Salmonella Typhimurium and Salmonella Kentucky isolates recovered from commercially processed chicken carcasses. J Food Prot. 2019;82(8):1364\u20138.","journal-title":"J Food Prot"},{"issue":"11","key":"2050_CR6","doi-asserted-by":"publisher","first-page":"e0242156","DOI":"10.1371\/journal.pone.0242156","volume":"15","author":"Y Chen","year":"2020","unstructured":"Chen Y, Liu H, Chen M, Sun HY, Wu YN. The human health burden of non-typhoidal Salmonella enterica and Vibrio parahaemolyticus foodborne gastroenteritis in Shanghai, east China. PLoS ONE. 2020;15(11):e0242156.","journal-title":"PLoS ONE"},{"issue":"1","key":"2050_CR7","doi-asserted-by":"publisher","first-page":"132","DOI":"10.3181\/00379727-86-21030","volume":"86","author":"M Bohnhoff","year":"1954","unstructured":"Bohnhoff M, Drake BL, Miller CP. Effect of streptomycin on susceptibility of intestinal tract to experimental Salmonella infection. Proc Soc Exp Biol Med. 1954;86(1):132\u20137.","journal-title":"Proc Soc Exp Biol Med"},{"key":"2050_CR8","doi-asserted-by":"publisher","first-page":"16215","DOI":"10.1038\/nmicrobiol.2016.215","volume":"2","author":"S Brugiroux","year":"2016","unstructured":"Brugiroux S, Beutler M, Pfann C, Garzetti D, Ruscheweyh HJ, Ring D, Diehl M, Herp S, Lotscher Y, Hussain S, et al. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat Microbiol. 2016;2:16215.","journal-title":"Nat Microbiol"},{"issue":"1","key":"2050_CR9","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.chom.2013.06.007","volume":"14","author":"E Deriu","year":"2013","unstructured":"Deriu E, Liu JZ, Pezeshki M, Edwards RA, Ochoa RJ, Contreras H, Libby SJ, Fang FC, Raffatellu M. Probiotic bacteria reduce Salmonella Typhimurium intestinal colonization by competing for iron. Cell Host Microbe. 2013;14(1):26\u201337.","journal-title":"Cell Host Microbe"},{"issue":"5","key":"2050_CR10","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1016\/j.chom.2019.03.004","volume":"25","author":"S Herp","year":"2019","unstructured":"Herp S, Brugiroux S, Garzetti D, Ring D, Jochum LM, Beutler M, Eberl C, Hussain S, Walter S, Gerlach RG, et al. Mucispirillum schaedleri antagonizes Salmonella virulence to protect mice against colitis. Cell Host Microbe. 2019;25(5):681-694 e688.","journal-title":"Cell Host Microbe"},{"issue":"6086","key":"2050_CR11","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.1126\/science.1222195","volume":"336","author":"N Kamada","year":"2012","unstructured":"Kamada N, Kim YG, Sham HP, Vallance BA, Puente JL, Martens EC, Nunez G. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science. 2012;336(6086):1325\u20139.","journal-title":"Science"},{"issue":"12","key":"2050_CR12","doi-asserted-by":"publisher","first-page":"e1004527","DOI":"10.1371\/journal.ppat.1004527","volume":"10","author":"LH Lam","year":"2014","unstructured":"Lam LH, Monack DM. Intraspecies competition for niches in the distal gut dictate transmission during persistent Salmonella infection. PLoS Pathog. 2014;10(12):e1004527.","journal-title":"PLoS Pathog"},{"issue":"6","key":"2050_CR13","doi-asserted-by":"publisher","first-page":"836","DOI":"10.1016\/j.chom.2022.04.012","volume":"30","author":"MJ Liou","year":"2022","unstructured":"Liou MJ, Miller BM, Litvak Y, Nguyen H, Natwick DE, Savage HP, Rixon JA, Mahan SP, Hiyoshi H, Rogers AWL, et al. Host cells subdivide nutrient niches into discrete biogeographical microhabitats for gut microbes. Cell Host Microbe. 2022;30(6):836-847 e836.","journal-title":"Cell Host Microbe"},{"issue":"1","key":"2050_CR14","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1016\/j.chom.2018.12.003","volume":"25","author":"Y Litvak","year":"2019","unstructured":"Litvak Y, Mon KKZ, Nguyen H, Chanthavixay G, Liou M, Velazquez EM, Kutter L, Alcantara MA, Byndloss MX, Tiffany CR, et al. Commensal Enterobacteriaceae protect against Salmonella colonization through oxygen competition. Cell Host Microbe. 2019;25(1):128-139 e125.","journal-title":"Cell Host Microbe"},{"issue":"6","key":"2050_CR15","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1016\/j.chom.2013.11.002","volume":"14","author":"L Maier","year":"2013","unstructured":"Maier L, Vyas R, Cordova CD, Lindsay H, Schmidt TS, Brugiroux S, Periaswamy B, Bauer R, Sturm A, Schreiber F, et al. Microbiota-derived hydrogen fuels Salmonella Typhimurium invasion of the gut ecosystem. Cell Host Microbe. 2013;14(6):641\u201351.","journal-title":"Cell Host Microbe"},{"issue":"6","key":"2050_CR16","doi-asserted-by":"publisher","first-page":"922","DOI":"10.1016\/j.chom.2020.04.013","volume":"27","author":"BD Nguyen","year":"2020","unstructured":"Nguyen BD, Cuenca VM, Hartl J, Gul E, Bauer R, Meile S, Ruthi J, Margot C, Heeb L, Besser F, et al. Import of aspartate and malate by DcuABC drives H(2)\/fumarate respiration to promote initial Salmonella gut-lumen colonization in mice. Cell Host Microbe. 2020;27(6):922-936 e926.","journal-title":"Cell Host Microbe"},{"issue":"6","key":"2050_CR17","doi-asserted-by":"publisher","first-page":"1057","DOI":"10.1038\/s41564-019-0407-8","volume":"4","author":"EM Velazquez","year":"2019","unstructured":"Velazquez EM, Nguyen H, Heasley KT, Saechao CH, Gil LM, Rogers AWL, Miller BM, Rolston MR, Lopez CA, Litvak Y, et al. Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection. Nat Microbiol. 2019;4(6):1057\u201364.","journal-title":"Nat Microbiol"},{"issue":"2","key":"2050_CR18","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1016\/j.chom.2018.07.002","volume":"24","author":"A Jacobson","year":"2018","unstructured":"Jacobson A, Lam L, Rajendram M, Tamburini F, Honeycutt J, Pham T, Van Treuren W, Pruss K, Stabler SR, Lugo K, et al. A gut commensal-produced metabolite mediates colonization resistance to Salmonella infection. Cell Host Microbe. 2018;24(2):296-307 e297.","journal-title":"Cell Host Microbe"},{"issue":"1","key":"2050_CR19","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1084\/jem.20181639","volume":"216","author":"MT Sorbara","year":"2019","unstructured":"Sorbara MT, Dubin K, Littmann ER, Moody TU, Fontana E, Seok R, Leiner IM, Taur Y, Peled JU, van den Brink MRM, et al. Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification. J Exp Med. 2019;216(1):84\u201398.","journal-title":"J Exp Med"},{"issue":"6351","key":"2050_CR20","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1126\/science.aam9949","volume":"357","author":"MX Byndloss","year":"2017","unstructured":"Byndloss MX, Olsan EE, Rivera-Chavez F, Tiffany CR, Cevallos SA, Lokken KL, Torres TP, Byndloss AJ, Faber F, Gao Y, et al. Microbiota-activated PPAR-gamma signaling inhibits dysbiotic Enterobacteriaceae expansion. Science. 2017;357(6351):570\u20135.","journal-title":"Science"},{"issue":"5790","key":"2050_CR21","doi-asserted-by":"publisher","first-page":"1126","DOI":"10.1126\/science.1127119","volume":"313","author":"HL Cash","year":"2006","unstructured":"Cash HL, Whitham CV, Behrendt CL, Hooper LV. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science. 2006;313(5790):1126\u201330.","journal-title":"Science"},{"issue":"6053","key":"2050_CR22","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1126\/science.1209791","volume":"334","author":"S Vaishnava","year":"2011","unstructured":"Vaishnava S, Yamamoto M, Severson KM, Ruhn KA, Yu X, Koren O, Ley R, Wakeland EK, Hooper LV. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science. 2011;334(6053):255\u20138.","journal-title":"Science"},{"issue":"1","key":"2050_CR23","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1128\/AEM.72.1.946-949.2006","volume":"72","author":"I Gantois","year":"2006","unstructured":"Gantois I, Ducatelle R, Pasmans F, Haesebrouck F, Hautefort I, Thompson A, Hinton JC, Van Immerseel F. Butyrate specifically down-regulates Salmonella pathogenicity island 1 gene expression. Appl Environ Microbiol. 2006;72(1):946\u20139.","journal-title":"Appl Environ Microbiol"},{"issue":"5","key":"2050_CR24","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1111\/mmi.12149","volume":"87","author":"CC Hung","year":"2013","unstructured":"Hung CC, Garner CD, Slauch JM, Dwyer ZW, Lawhon SD, Frye JG, McClelland M, Ahmer BM, Altier C. The intestinal fatty acid propionate inhibits Salmonella invasion through the post-translational control of HilD. Mol Microbiol. 2013;87(5):1045\u201360.","journal-title":"Mol Microbiol"},{"issue":"1","key":"2050_CR25","doi-asserted-by":"publisher","first-page":"e0190613","DOI":"10.1371\/journal.pone.0190613","volume":"13","author":"N Kohli","year":"2018","unstructured":"Kohli N, Crisp Z, Riordan R, Li M, Alaniz RC, Jayaraman A. The microbiota metabolite indole inhibits Salmonella virulence: involvement of the PhoPQ two-component system. PLoS ONE. 2018;13(1):e0190613.","journal-title":"PLoS ONE"},{"issue":"1","key":"2050_CR26","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/s41589-019-0392-5","volume":"16","author":"ZJ Zhang","year":"2020","unstructured":"Zhang ZJ, Pedicord VA, Peng T, Hang HC. Site-specific acylation of a bacterial virulence regulator attenuates infection. Nat Chem Biol. 2020;16(1):95\u2013103.","journal-title":"Nat Chem Biol"},{"issue":"6","key":"2050_CR27","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1016\/j.chom.2017.05.005","volume":"21","author":"S Thiemann","year":"2017","unstructured":"Thiemann S, Smit N, Roy U, Lesker TR, Galvez EJC, Helmecke J, Basic M, Bleich A, Goodman AL, Kalinke U, et al. Enhancement of IFNgamma production by distinct commensals ameliorates Salmonella-induced disease. Cell Host Microbe. 2017;21(6):682-694 e685.","journal-title":"Cell Host Microbe"},{"issue":"3","key":"2050_CR28","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1016\/j.cell.2009.09.033","volume":"139","author":"II Ivanov","year":"2009","unstructured":"Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, Wei D, Goldfarb KC, Santee CA, Lynch SV, et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009;139(3):485\u201398.","journal-title":"Cell"},{"issue":"3","key":"2050_CR29","doi-asserted-by":"publisher","first-page":"eaai7732","DOI":"10.1126\/sciimmunol.aai7732","volume":"1","author":"VA Pedicord","year":"2016","unstructured":"Pedicord VA, Lockhart AAK, Rangan KJ, Craig JW, Loschko J, Rogoz A, Hang HC, Mucida D. Exploiting a host-commensal interaction to promote intestinal barrier function and enteric pathogen tolerance. Sci Immunol. 2016;1(3):eaai7732.","journal-title":"Sci Immunol"},{"issue":"6306","key":"2050_CR30","doi-asserted-by":"publisher","first-page":"1434","DOI":"10.1126\/science.aaf3552","volume":"353","author":"KJ Rangan","year":"2016","unstructured":"Rangan KJ, Pedicord VA, Wang YC, Kim B, Lu Y, Shaham S, Mucida D, Hang HC. A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens. Science. 2016;353(6306):1434\u20137.","journal-title":"Science"},{"key":"2050_CR31","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1007\/978-1-4615-4143-1_28","volume":"473","author":"RM Tsolis","year":"1999","unstructured":"Tsolis RM, Kingsley RA, Townsend SM, Ficht TA, Adams LG, Baumler AJ. Of mice, calves, and men. Comparison of the mouse typhoid model with other Salmonella infections. Adv Exp Med Biol. 1999;473:261\u201374.","journal-title":"Adv Exp Med Biol"},{"issue":"5","key":"2050_CR32","doi-asserted-by":"publisher","first-page":"1806","DOI":"10.1128\/IAI.01369-10","volume":"79","author":"RM Tsolis","year":"2011","unstructured":"Tsolis RM, Xavier MN, Santos RL, Baumler AJ. How to become a top model: impact of animal experimentation on human Salmonella disease research. Infect Immun. 2011;79(5):1806\u201314.","journal-title":"Infect Immun"},{"issue":"5","key":"2050_CR33","doi-asserted-by":"publisher","first-page":"2839","DOI":"10.1128\/IAI.71.5.2839-2858.2003","volume":"71","author":"M Barthel","year":"2003","unstructured":"Barthel M, Hapfelmeier S, Quintanilla-Martinez L, Kremer M, Rohde M, Hogardt M, Pfeffer K, Russmann H, Hardt WD. Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host. Infect Immun. 2003;71(5):2839\u201358.","journal-title":"Infect Immun"},{"key":"2050_CR34","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1093\/infdis\/111.2.117","volume":"111","author":"M Bohnhoff","year":"1962","unstructured":"Bohnhoff M, Miller CP. Enhanced susceptibility to Salmonella infection in streptomycin-treated mice. J Infect Dis. 1962;111:117\u201327.","journal-title":"J Infect Dis"},{"issue":"1","key":"2050_CR35","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.chom.2021.12.003","volume":"30","author":"BS Beresford-Jones","year":"2022","unstructured":"Beresford-Jones BS, Forster SC, Stares MD, Notley G, Viciani E, Browne HP, Boehmler DJ, Soderholm AT, Kumar N, Vervier K, et al. The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. Cell Host Microbe. 2022;30(1):124-138 e128.","journal-title":"Cell Host Microbe"},{"issue":"3","key":"2050_CR36","doi-asserted-by":"publisher","first-page":"151484","DOI":"10.1016\/j.ijmm.2021.151484","volume":"311","author":"B Stecher","year":"2021","unstructured":"Stecher B. Establishing causality in Salmonella-microbiota-host interaction: the use of gnotobiotic mouse models and synthetic microbial communities. Int J Med Microbiol. 2021;311(3):151484.","journal-title":"Int J Med Microbiol"},{"issue":"11","key":"2050_CR37","doi-asserted-by":"publisher","first-page":"1680","DOI":"10.1016\/j.chom.2021.09.004","volume":"29","author":"C Eberl","year":"2021","unstructured":"Eberl C, Weiss AS, Jochum LM, Durai Raj AC, Ring D, Hussain S, Herp S, Meng C, Kleigrewe K, Gigl M, et al. E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source. Cell Host Microbe. 2021;29(11):1680-16921 e687.","journal-title":"Cell Host Microbe"},{"issue":"3","key":"2050_CR38","doi-asserted-by":"publisher","first-page":"1675","DOI":"10.4049\/jimmunol.174.3.1675","volume":"174","author":"S Hapfelmeier","year":"2005","unstructured":"Hapfelmeier S, Stecher B, Barthel M, Kremer M, Muller AJ, Heikenwalder M, Stallmach T, Hensel M, Pfeffer K, Akira S, et al. The Salmonella pathogenicity island (SPI)-2 and SPI-1 type III secretion systems allow Salmonella serovar typhimurium to trigger colitis via MyD88-dependent and MyD88-independent mechanisms. J Immunol. 2005;174(3):1675\u201385.","journal-title":"J Immunol"},{"issue":"42","key":"2050_CR39","doi-asserted-by":"publisher","first-page":"11027","DOI":"10.1073\/pnas.1711395114","volume":"114","author":"DC Propheter","year":"2017","unstructured":"Propheter DC, Chara AL, Harris TA, Ruhn KA, Hooper LV. Resistin-like molecule beta is a bactericidal protein that promotes spatial segregation of the microbiota and the colonic epithelium. Proc Natl Acad Sci U S A. 2017;114(42):11027\u201333.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"2050_CR40","doi-asserted-by":"publisher","first-page":"920","DOI":"10.1007\/s00595-020-01974-z","volume":"50","author":"K Watanabe","year":"2020","unstructured":"Watanabe K, Itoh K, Park SH, Kaku M, Ishii K, Sasano H, Naitoh T, Unno M, Fukushima K. Resistin-like molecule beta, a colonic epithelial protein, exhibits antimicrobial activity against Staphylococcus aureus including methicillin-resistant strains. Surg Today. 2020;50(8):920\u201330.","journal-title":"Surg Today"},{"issue":"1","key":"2050_CR41","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1016\/j.jaci.2006.04.039","volume":"118","author":"SP Hogan","year":"2006","unstructured":"Hogan SP, Seidu L, Blanchard C, Groschwitz K, Mishra A, Karow ML, Ahrens R, Artis D, Murphy AJ, Valenzuela DM, et al. Resistin-like molecule beta regulates innate colonic function: barrier integrity and inflammation susceptibility. J Allergy Clin Immunol. 2006;118(1):257\u201368.","journal-title":"J Allergy Clin Immunol"},{"issue":"8","key":"2050_CR42","doi-asserted-by":"publisher","first-page":"e1005108","DOI":"10.1371\/journal.ppat.1005108","volume":"11","author":"KS Bergstrom","year":"2015","unstructured":"Bergstrom KS, Morampudi V, Chan JM, Bhinder G, Lau J, Yang H, Ma C, Huang T, Ryz N, Sham HP, et al. Goblet cell derived RELM-beta recruits CD4+ T cells during infectious colitis to promote protective intestinal epithelial cell proliferation. PLoS Pathog. 2015;11(8):e1005108.","journal-title":"PLoS Pathog"},{"issue":"2","key":"2050_CR43","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1073\/pnas.98.2.502","volume":"98","author":"CM Steppan","year":"2001","unstructured":"Steppan CM, Brown EJ, Wright CM, Bhat S, Banerjee RR, Dai CY, Enders GH, Silberg DG, Wen X, Wu GD, et al. A family of tissue-specific resistin-like molecules. Proc Natl Acad Sci U S A. 2001;98(2):502\u20136.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"2050_CR44","doi-asserted-by":"publisher","first-page":"971","DOI":"10.1016\/j.jcmgh.2022.11.004","volume":"15","author":"MA Schumacher","year":"2023","unstructured":"Schumacher MA, Liu CY, Katada K, Thai MH, Hsieh JJ, Hansten BJ, Waddell A, Rosen MJ, Frey MR. Deep Crypt secretory cell differentiation in the colonic epithelium is regulated by Sprouty2 and interleukin 13. Cell Mol Gastroenterol Hepatol. 2023;15(4):971\u201384.","journal-title":"Cell Mol Gastroenterol Hepatol"},{"issue":"37","key":"2050_CR45","doi-asserted-by":"publisher","first-page":"E5399","DOI":"10.1073\/pnas.1607327113","volume":"113","author":"N Sasaki","year":"2016","unstructured":"Sasaki N, Sachs N, Wiebrands K, Ellenbroek SI, Fumagalli A, Lyubimova A, Begthel H, van den Born M, van Es JH, Karthaus WR, et al. Reg4+ deep crypt secretory cells function as epithelial niche for Lgr5+ stem cells in colon. Proc Natl Acad Sci U S A. 2016;113(37):E5399-5407.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"2050_CR46","doi-asserted-by":"publisher","first-page":"836","DOI":"10.1038\/s41467-021-21113-7","volume":"12","author":"MA Schumacher","year":"2021","unstructured":"Schumacher MA, Hsieh JJ, Liu CY, Appel KL, Waddell A, Almohazey D, Katada K, Bernard JK, Bucar EB, Gadeock S, et al. Sprouty2 limits intestinal tuft and goblet cell numbers through GSK3beta-mediated restriction of epithelial IL-33. Nat Commun. 2021;12(1):836.","journal-title":"Nat Commun"},{"issue":"6","key":"2050_CR47","doi-asserted-by":"publisher","first-page":"G493","DOI":"10.1152\/ajpgi.00093.2023","volume":"325","author":"MA Schumacher","year":"2023","unstructured":"Schumacher MA. The emerging roles of deep crypt secretory cells in colonic physiology. Am J Physiol Gastrointest Liver Physiol. 2023;325(6):G493\u2013500.","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"issue":"6","key":"2050_CR48","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1038\/s41385-020-0299-1","volume":"13","author":"SL Clay","year":"2020","unstructured":"Clay SL, Bravo-Blas A, Wall DM, MacLeod MKL, Milling SWF. Regulatory T cells control the dynamic and site-specific polarization of total CD4 T cells following Salmonella infection. Mucosal Immunol. 2020;13(6):946\u201357.","journal-title":"Mucosal Immunol"},{"issue":"27","key":"2050_CR49","doi-asserted-by":"publisher","first-page":"12204","DOI":"10.1073\/pnas.0909122107","volume":"107","author":"JL Round","year":"2010","unstructured":"Round JL, Mazmanian SK. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A. 2010;107(27):12204\u20139.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6015","key":"2050_CR50","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1126\/science.1198469","volume":"331","author":"K Atarashi","year":"2011","unstructured":"Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, Cheng G, Yamasaki S, Saito T, Ohba Y, et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science. 2011;331(6015):337\u201341.","journal-title":"Science"},{"issue":"5","key":"2050_CR51","doi-asserted-by":"publisher","first-page":"794","DOI":"10.1016\/j.immuni.2011.03.021","volume":"34","author":"MB Geuking","year":"2011","unstructured":"Geuking MB, Cahenzli J, Lawson MA, Ng DC, Slack E, Hapfelmeier S, McCoy KD, Macpherson AJ. Intestinal bacterial colonization induces mutualistic regulatory T cell responses. Immunity. 2011;34(5):794\u2013806.","journal-title":"Immunity"},{"issue":"6145","key":"2050_CR52","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1126\/science.1241165","volume":"341","author":"PM Smith","year":"2013","unstructured":"Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA, Bohlooly YM, Glickman JN, Garrett WS. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science. 2013;341(6145):569\u201373.","journal-title":"Science"},{"issue":"7480","key":"2050_CR53","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1038\/nature12721","volume":"504","author":"Y Furusawa","year":"2013","unstructured":"Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G, Takahashi D, Nakanishi Y, Uetake C, Kato K, Kato T, et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature. 2013;504(7480):446\u201350.","journal-title":"Nature"},{"issue":"9","key":"2050_CR54","doi-asserted-by":"publisher","first-page":"1895","DOI":"10.1038\/s12276-023-00985-3","volume":"55","author":"I Kang","year":"2023","unstructured":"Kang I, Kim Y, Lee HK. Double-edged sword: gammadelta T cells in mucosal homeostasis and disease. Exp Mol Med. 2023;55(9):1895\u2013904.","journal-title":"Exp Mol Med"},{"issue":"Pt 6","key":"2050_CR55","doi-asserted-by":"publisher","first-page":"2141","DOI":"10.1099\/00207713-52-6-2141","volume":"52","author":"SH Duncan","year":"2002","unstructured":"Duncan SH, Hold GL, Harmsen HJM, Stewart CS, Flint HJ. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int J Syst Evol Microbiol. 2002;52(Pt 6):2141\u20136.","journal-title":"Int J Syst Evol Microbiol"},{"issue":"2","key":"2050_CR56","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1128\/AEM.06858-11","volume":"78","author":"M Lopez-Siles","year":"2012","unstructured":"Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJ, Garcia-Gil LJ, Flint HJ. Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl Environ Microbiol. 2012;78(2):420\u20138.","journal-title":"Appl Environ Microbiol"},{"issue":"Pt 11","key":"2050_CR57","doi-asserted-by":"publisher","first-page":"3651","DOI":"10.1099\/00221287-148-11-3651","volume":"148","author":"NH Salzman","year":"2002","unstructured":"Salzman NH, de Jong H, Paterson Y, Harmsen HJM, Welling GW, Bos NA. Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria. Microbiology (Reading). 2002;148(Pt 11):3651\u201360.","journal-title":"Microbiology (Reading)"},{"issue":"7","key":"2050_CR58","doi-asserted-by":"publisher","first-page":"3380","DOI":"10.1128\/JCM.43.7.3380-3389.2005","volume":"43","author":"A Swidsinski","year":"2005","unstructured":"Swidsinski A, Weber J, Loening-Baucke V, Hale LP, Lochs H. Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J Clin Microbiol. 2005;43(7):3380\u20139.","journal-title":"J Clin Microbiol"},{"issue":"8","key":"2050_CR59","doi-asserted-by":"publisher","first-page":"e12238","DOI":"10.1371\/journal.pone.0012238","volume":"5","author":"ME Johansson","year":"2010","unstructured":"Johansson ME, Gustafsson JK, Sjoberg KE, Petersson J, Holm L, Sjovall H, Hansson GC. Bacteria penetrate the inner mucus layer before inflammation in the dextran sulfate colitis model. PLoS ONE. 2010;5(8):e12238.","journal-title":"PLoS ONE"},{"issue":"1","key":"2050_CR60","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1186\/s12866-021-02118-0","volume":"21","author":"R Cao","year":"2021","unstructured":"Cao R, Bao L, Pan M, Zhang C, Liao H, Liu L, Li Y, Li M. Detection of SARS-CoV-2 in fecal samples with different pretreatment methods and PCR kits. BMC Microbiol. 2021;21(1):56.","journal-title":"BMC Microbiol"},{"key":"2050_CR61","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1186\/1471-2105-13-134","volume":"13","author":"J Ye","year":"2012","unstructured":"Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 2012;13:134.","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"2050_CR62","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","volume":"14","author":"R Patro","year":"2017","unstructured":"Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14(4):417\u20139.","journal-title":"Nat Methods"},{"issue":"12","key":"2050_CR63","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.","journal-title":"Genome Biol"},{"issue":"1","key":"2050_CR64","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1002\/pro.4218","volume":"31","author":"PD Thomas","year":"2022","unstructured":"Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou LP, Mi H. PANTHER: making genome-scale phylogenetics accessible to all. Protein Sci. 2022;31(1):8\u201322.","journal-title":"Protein Sci"},{"issue":"3","key":"2050_CR65","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1038\/s41596-019-0128-8","volume":"14","author":"H Mi","year":"2019","unstructured":"Mi H, Muruganujan A, Huang X, Ebert D, Mills C, Guo X, Thomas PD. Protocol update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). Nat Protoc. 2019;14(3):703\u201321.","journal-title":"Nat Protoc"}],"container-title":["Microbiome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-025-02050-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40168-025-02050-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-025-02050-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,3]],"date-time":"2025-03-03T15:11:41Z","timestamp":1741014701000},"score":1,"resource":{"primary":{"URL":"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-025-02050-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,28]]},"references-count":65,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["2050"],"URL":"https:\/\/doi.org\/10.1186\/s40168-025-02050-9","relation":{},"ISSN":["2049-2618"],"issn-type":[{"value":"2049-2618","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,28]]},"assertion":[{"value":"22 May 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 January 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 February 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Mice were maintained at the Home Office-approved Wellcome Sanger Institute mouse facility, and all procedures were carried out in accordance with the United Kingdom Animals (Scientific Procedures) Act of 1986.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"TDL is a founder and CSO of Microbiotica. The other authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"61"}}