Archaea influence composition of endoscopically visible ileocolonic biofilms

References

• Oka P, Parr H, Barberio B, Black CJ, Savarino EV, Ford AC. Global prevalence of irritable bowel syndrome according to Rome III or IV criteria: a systematic review and meta-analysis. Lancet Gastroenterol Hepatol [Internet]. 2020;5(10):908–14. doi:10.1016/S2468-1253(20)30217-X.
   PubMed Web of Science ®Google Scholar
• Lovell RM, Ford AC. Global prevalence of and risk factors for irritable bowel syndrome: a meta-analysis. Clin Gastroenterol Hepatol [Internet]. 2012;10(7):712–721. doi:10.1016/j.cgh.2012.02.029.
   PubMed Web of Science ®Google Scholar
• Enck P, Aziz Q, Barbara G, Farmer AD, Fukudo S, Mayer EA, Niesler B, Quigley EMM, Rajilić-Stojanović M, Schemann M. et al. Irritable bowel syndrome. Nat Rev Dis Primers. 2016;2(1):16014. doi:10.1038/nrdp.2016.14.
   PubMedGoogle Scholar
• Kaplan GG. The global burden of IBD: From 2015 to 2025. Nat Rev Gastroenterol Hepatol [Internet]. 2015;12(12):720–727. doi:10.1038/nrgastro.2015.150.
   PubMed Web of Science ®Google Scholar
• Kobayashi T, Siegmund B, Le Berre C, Wei SC, Ferrante M, Shen B, Bernstein CN, Danese S, Peyrin-Biroulet L, Hibi T. et al. Ulcerative colitis. Nat Rev Dis Primers [Internet]. 2020;6(1). doi:10.1038/s41572-020-0205-x.
   PubMedGoogle Scholar
• Roda G, Chien Ng S, Kotze PG, Argollo M, Panaccione R, Spinelli A, Kaser A, Peyrin-Biroulet L, Danese S. Crohn’s disease. Nat Rev Dis Primers [Internet]. 2020;6(1). doi:10.1038/s41572-020-0156-2.
   Google Scholar
• Dammann K, Khare V, Gasche C. Tracing PAKs from GI inflammation to cancer. Gut. 2014;63(7):1173–1184. doi:10.1136/gutjnl-2014-306768.
   PubMed Web of Science ®Google Scholar
• Frick A, Khare V, Paul G, Lang M, Ferk F, Knasmüller S, Beer A, Oberhuber, G Gasche, C. Overt increase of oxidative stress and DNA damage in murine and human colitis and colitis-associated neoplasia. Mol Cancer Res. 2018;16(4):634–642. doi:10.1158/1541-7786.MCR-17-0451.
   PubMed Web of Science ®Google Scholar
• Shah SC, Itzkowitz SH. Colorectal cancer in inflammatory bowel disease: mechanisms and management. Gastroenterology [Internet]. 2022;162(3):715–730.e3. doi:10.1053/j.gastro.2021.10.035.
   PubMed Web of Science ®Google Scholar
• Ullman TA, Itzkowitz SH. Intestinal inflammation and cancer. Gastroenterology [Internet]. 2011;140(6):1807–1816.e1. doi:10.1053/j.gastro.2011.01.057.
   PubMed Web of Science ®Google Scholar
• Frick A, Khare V, Jimenez K, Dammann K, Lang M, Krnjic A, Gmainer C, Baumgartner M, Mesteri I, Gasche C. A novel PAK1–Notch1 axis regulates crypt homeostasis in intestinal inflammation. Cmgh [Internet]. 2021;11(3):892–907.e1. doi:10.1016/j.jcmgh.2020.11.001.
   Google Scholar
• Rajilić-Stojanović M, Biagi E, Heilig HGHJ, Kajander K, Kekkonen RA, Tims S, de Vos WM. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome. Gastroenterology. 2011;141(5):1792–1801. doi:10.1053/j.gastro.2011.07.043.
   PubMed Web of Science ®Google Scholar
• Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569(7758):655–662. doi:10.1038/s41586-019-1237-9.
   PubMed Web of Science ®Google Scholar
• Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF. et al. Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Sci Transl Med. 2018;10(472):1–12. doi:10.1126/scitranslmed.aap8914.
   Web of Science ®Google Scholar
• Pittayanon R, Lau JT, Leontiadis GI, Tse F, Yuan Y, Surette M, Moayyedi P. Differences in gut microbiota in patients with vs without inflammatory bowel diseases: a systematic review. Gastroenterology [Internet]. 2020;158(4):930–946.e1. doi:10.1053/j.gastro.2019.11.294.
   PubMed Web of Science ®Google Scholar
• Pittayanon R, Lau JT, Yuan Y, Leontiadis GI, Tse F, Surette M, Moayyedi P. Gut microbiota in patients with irritable bowel syndrome—a systematic review. Gastroenterology [Internet]. 2019;157(1):97–108. doi:10.1053/j.gastro.2019.03.049.
   PubMed Web of Science ®Google Scholar
• Moayyedi P, Surette MG, Kim PT, Libertucci J, Wolfe M, Onischi C, Armstrong D, Marshall JK, Kassam Z, Reinisch W. et al. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology [Internet]. 2015;149(1):102–109.e6. doi:10.1053/j.gastro.2015.04.001.
   PubMed Web of Science ®Google Scholar
• Johnsen PH, Hilpüsch F, Cavanagh JP, Leikanger IS, Kolstad C, Valle PC, Goll R. Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial. Lancet Gastroenterol Hepatol. 2018;3(1):17–24. doi:10.1016/S2468-1253(17)30338-2.
   PubMed Web of Science ®Google Scholar
• Borrel G, Brugère JF, Gribaldo S, Schmitz RA, Moissl-Eichinger C. The host-associated archaeome. Nat Rev Microbiol. 2020;18(11):622–636. doi:10.1038/s41579-020-0407-y.
   PubMed Web of Science ®Google Scholar
• Hoegenauer C, Hammer HF, Mahnert A, Moissl-Eichinger C. Methanogenic archaea in the human gastrointestinal tract. Nat Rev Gastroenterol Hepatol. 2022;19(12):805–813. doi:10.1038/s41575-022-00673-z.
   PubMed Web of Science ®Google Scholar
• Botschuijver S, Roeselers G, Levin E, Jonkers DM, Welting O, Heinsbroek SEM, de Weerd HH, Boekhout T, Fornai M, Masclee AA. et al. Intestinal fungal dysbiosis is associated with visceral hypersensitivity in patients with irritable bowel syndrome and rats. Gastroenterology [Internet]. 2017;153(4):1026–1039. doi:10.1053/j.gastro.2017.06.004.
   PubMed Web of Science ®Google Scholar
• Ghoshal U, Shukla R, Srivastava D, Ghoshal UC. Irritable bowel syndrome, particularly the constipation-predominant form, involves an increase in Methanobrevibacter smithii, which is associated with higher methane production. Gut Liver. 2016;10(6):932–938. doi:10.5009/gnl15588.
   PubMed Web of Science ®Google Scholar
• Lecours PB, Marsolais D, Cormier Y, Berberi M, Haché C, Bourdages R, Duchaine C. Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases. PLoS One. 2014;9(2):e87734. doi:10.1371/journal.pone.0087734.
   PubMed Web of Science ®Google Scholar
• Sokol H, Leducq V, Aschard H, Pham HP, Jegou S, Landman C, Cohen D, Liguori G, Bourrier A, Nion-Larmurier I. et al. Fungal microbiota dysbiosis in IBD. Gut. 2017;66(6):1039–1048. doi:10.1136/gutjnl-2015-310746.
   PubMed Web of Science ®Google Scholar
• Jalanka-Tuovinen J, Salojärvi J, Salonen A, Immonen O, Garsed K, Kelly FM, Zaitoun A, Palva A, Spiller RC, de Vos WM. et al. Faecal microbiota composition and host–microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome. Gut. 2014;63(11):1737–1745. doi:10.1136/gutjnl-2013-305994.
   PubMed Web of Science ®Google Scholar
• Koskinen K, Pausan MR, Perras A, Beck M, Bang C, Mora M, Schilhabel A, Schmitz R, Moissl-Eichinger C. et al. First insights into the diverse human archaeome: specific detection of archaea in the gastrointestinal tract, lung, and nose and on skin. MBio. 2017;8(6):e00824–17. doi:10.1128/mBio.00824-17.
   PubMed Web of Science ®Google Scholar
• Friedman ES, Bittinger K, Esipova TV, Hou L, Chau L, Jiang J, Mesaros C, Lund PJ, Liang X, FitzGerald GA. et al. Microbes vs. chemistry in the origin of the anaerobic gut lumen. Proc Natl Acad Sci U S A. 2018;115(16):4170–4175. doi:10.1073/pnas.1718635115.
   PubMed Web of Science ®Google Scholar
• Sundin OH, Mendoza-Ladd A, Zeng M, Diaz-Arévalo D, Morales E, Fagan BM, Ordoñez J, Velez P, Antony N, McCallum RW. et al. The human jejunum has an endogenous microbiota that differs from those in the oral cavity and colon. BMC Microbiol. 2017;17(1):1–17. doi:10.1186/s12866-017-1059-6.
   PubMedGoogle Scholar
• Tropini C, Earle KA, Huang KC, Sonnenburg JL. The gut microbiome: connecting spatial organization to Function. Cell Host Microbe [Internet]. 2017;21(4):433–442. doi:10.1016/j.chom.2017.03.010.
   PubMed Web of Science ®Google Scholar
• Lee J-Y, Tsolis RM, Bäumler AJ. The microbiome and gut homeostasis. Science (80-) [Internet]. 2022;377(6601). doi:10.1126/science.abp9960.
   Web of Science ®Google Scholar
• Baumgartner M, Lang M, Holley H, Crepaz D, Hausmann B, Pjevac P, Moser D, Haller F, Hof F, Beer A. et al. Mucosal biofilms are an endoscopic feature of irritable bowel syndrome and ulcerative colitis. Gastroenterology [Internet]. 2021; 1–12. doi:10.1053/j.gastro.2021.06.024.
   Google Scholar
• Toole GO, Kaplan HB, Kolter R. Biofilm formation as microbial development. Annu Rev Microbiol. 2000;54(1):49–79. doi:10.1146/annurev.micro.54.1.49.
   PubMedGoogle Scholar
• Hall-Stoodley L, Costerton JW, Stoodley P. Bacterial biofilms: From the natural environment to infectious diseases. Nat Rev Microbiol. 2004;2(2):95–108. doi:10.1038/nrmicro821.
   PubMed Web of Science ®Google Scholar
• Watnick P, Kolter KR. Biofilm, city of microbes. J Bacteriol. 2000;182(10):2675–2679. doi:10.1128/JB.182.10.2675-2679.2000.
   PubMed Web of Science ®Google Scholar
• Wong B, Camilleri M, Carlson P, McKinzie S, Busciglio I, Bondar O, Dyer RB, Lamsam J, Zinsmeister AR. Increased bile acid biosynthesis is associated with irritable bowel syndrome with diarrhea. Clin Gastroenterol Hepatol. 2012;10(9):1009–15e3. doi:10.1016/j.cgh.2012.05.006.
   PubMed Web of Science ®Google Scholar
• Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH. et al. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput Biol [Internet]. 2021;17(11):1–27. doi:10.1371/journal.pcbi.1009442.
   Web of Science ®Google Scholar
• Drewes JL, White JR, Dejea CM, Fathi P, Iyadorai T, Vadivelu J, Roslani AC, Wick EC, Mongodin EF, Loke MF. et al. High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia. npj Biofilms Microbiomes [Internet]. 2017;3(1). doi:10.1038/s41522-017-0040-3.
   Google Scholar
• Dejea CM, Wick EC, Hechenbleikner EM, White JR, Mark Welch JL, Rossetti BJ, Peterson SN, Snesrud EC, Borisy GG, Lazarev M. et al. Microbiota organization is a distinct feature of proximal colorectal cancers. Proc Natl Acad Sci U S A. 2014;111(51):18321–18326. doi:10.1073/pnas.1406199111.
   PubMed Web of Science ®Google Scholar
• Dejea CM, Fathi P, Craig JM, Boleij A, Taddese R, Geis AL, Wu X, DeStefano Shields CE, Hechenbleikner EM, Huso DL. et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science (80-). 2018;359(6375):592–597. doi:10.1126/science.aah3648.
   PubMed Web of Science ®Google Scholar
• Motta JP, Wallace JL, Buret AG, Deraison C, Vergnolle N. Gastrointestinal biofilms in health and disease. Nat Rev Gastroenterol Hepatol [Internet]. 2021;18(5):314–334. doi:10.1038/s41575-020-00397-y.
   PubMed Web of Science ®Google Scholar
• Mar Rodríguez M, Pérez D, Javier Chaves F, Esteve E, Marin-Garcia P, Xifra G, Vendrell J, Jové M, Pamplona R, Ricart W. et al. Obesity changes the human gut mycobiome. Sci Rep. 2015;5(1):1–15. doi:10.1038/srep14600.
   Google Scholar
• Lee JY, Cevallos SA, Byndloss MX, Tiffany CR, Olsan EE, Butler BP, Young BM, Rogers AWL, Nguyen H, Kim K. et al. High-fat diet and antibiotics cooperatively impair mitochondrial bioenergetics to trigger dysbiosis that exacerbates pre-inflammatory bowel disease. Cell Host Microbe. 2020;28(2):273–284.e6. doi:10.1016/j.chom.2020.06.001.
   PubMed Web of Science ®Google Scholar
• Gulhane M, Murray L, Lourie R, Tong H, Sheng YH, Wang R, Kang A, Schreiber V, Wong KY, Magor G. et al. High fat diets induce colonic epithelial cell stress and inflammation that is reversed by IL-22. Sci Rep [Internet]. 2016;6(1):1–17. doi:10.1038/srep28990.
   PubMedGoogle Scholar
• Crost EH, Tailford LE, Monestier M, Swarbreck D, Henrissat B, Crossman LC, Juge N. The mucin-degradation strategy of Ruminococcus gnavus: The importance of intramolecular trans-sialidases. Gut Microbes [Internet]. 2016;7(4):302–312. doi:10.1080/19490976.2016.1186334.
   PubMed Web of Science ®Google Scholar
• Chand D, Avinash VS, Yadav Y, Pundle AV, Suresh CG, Ramasamy S. Molecular features of bile salt hydrolases and relevance in human health. Biochim Biophys Acta – Gen Subj [Internet]. 2017;1861(1):2981–2991. doi:10.1016/j.bbagen.2016.09.024.
   PubMed Web of Science ®Google Scholar
• Pumbwe L, Skilbeck CA, Nakano V, Avila-Campos MJ, Piazza RMF, Wexler HM. Bile salts enhance bacterial co-aggregation, bacterial-intestinal epithelial cell adhesion, biofilm formation and antimicrobial resistance of Bacteroides fragilis. Microb Pathog. 2007;43(2):78–87. doi:10.1016/j.micpath.2007.04.002.
   PubMed Web of Science ®Google Scholar
• Madigan KE, Richa Bundy RBW. Distinctive clinical correlates of small intestinal bacterial overgrowth with methanogens. Clin Gastroenterol Hepatol. 2021;20(7):1598–1605. doi:10.1016/j.cgh.2021.09.035.
   PubMed Web of Science ®Google Scholar
• Gandhi A, Shah A, Jones MP, Koloski N, Talley NJ, Morrison M, Holtmann G. Methane positive small intestinal bacterial overgrowth in inflammatory bowel disease and irritable bowel syndrome: A systematic review and meta-analysis. Gut Microbes [Internet]. 2021;13(1):1–16. doi:10.1080/19490976.2021.1933313.
   Web of Science ®Google Scholar