The diagnostic and prognostic potential of gut bacteria in inflammatory bowel disease

References

• Schirmer M, Garner A, Vlamakis H, Xavier RJ. Microbial genes and pathways in inflammatory bowel disease. Nat Rev Microbiol [Internet] 2019; 17:497–28. Available from: http://www.nature.com/articles/s41579-019-0213-6
   PubMed Web of Science ®Google Scholar
• Kåhrström CT, Pariente N, Weiss U. Intestinal microbiota in health and disease. Nature [Internet] 2016; 535:47. Available from: http://www.nature.com/articles/535047a
   PubMed Web of Science ®Google Scholar
• Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol [Internet] 2021; 19:55–71. Available from: http://www.ncbi.nlm.nih.gov/pubmed/32887946
   PubMed Web of Science ®Google Scholar
• Nathan NN, Philpott DJ, Girardin SE. The intestinal microbiota: from health to disease, and back. Microbes Infect [Internet] 2021; 23:104849. Available from: https://linkinghub.elsevier.com/retrieve/pii/S128645792100071X
   PubMed Web of Science ®Google Scholar
• Marchesi JR, Adams DH, Fava F, Hermes GDA, Hirschfield GM, Hold G, Quraishi MN, Kinross J, Smidt H, Tuohy KM, et al. The gut microbiota and host health: a new clinical frontier. Gut [Internet] 2016; 65:330–339. Available from:
   PubMed Web of Science ®Google Scholar
• Lavelle A, Sokol H. Gut microbiota-derived metabolites as key actors in inflammatory bowel disease. Nat Rev Gastroenterol Hepatol [Internet] 2020; 17:223–237. Available from: http://www.nature.com/articles/s41575-019-0258-z
   PubMed Web of Science ®Google Scholar
• Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol [Internet] 2016; 16:341–352. Available from: http://www.nature.com/articles/nri.2016.42
   PubMed Web of Science ®Google Scholar
• Litvak Y, Bäumler AJ. Microbiota-nourishing immunity: a Guide to understanding our microbial self. Immunity [Internet] 2019; 51:214–224. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1074761319303292
   PubMed Web of Science ®Google Scholar
• Weingarden AR, Vaughn BP. Intestinal microbiota, fecal microbiota transplantation, and inflammatory bowel disease. Gut Microbes [Internet] 2017; 8:238–252. Available from: https://www.tandfonline.com/doi/full/10.1080/19490976.2017.1290757
   PubMed Web of Science ®Google Scholar
• Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol [Internet] 2019; 4:293–305.
   PubMed Web of Science ®Google Scholar
• Vich VA, 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 [Internet] 2018; 10. Available from: https://www.science.org/doi/10.1126/scitranslmed.aap8914.
   Web of Science ®Google Scholar
• Alam MT, Amos GCA, Murphy ARJ, Murch S, Wellington EMH, Arasaradnam RP. Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels. Gut Pathog [Internet] 2020; 12:1.Available from: https://gutpathogens.biomedcentral.com/articles/10.1186/s13099-019-0341-6
   PubMed Web of Science ®Google Scholar
• Stange EF, Schroeder BO. Microbiota and mucosal defense in IBD: an update. Expert Rev Gastroenterol Hepatol [Internet] 2019; 13:963–976. Available from: https://www.tandfonline.com/doi/full/10.1080/17474124.2019.1671822
   PubMed Web of Science ®Google Scholar
• Casén C, Vebø HC, Sekelja M, Hegge FT, Karlsson MK, Ciemniejewska E, Dzankovic S, Frøyland C, Nestestog R, Engstrand L, et al. Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD. Aliment Pharmacol Ther [Internet] 2015; 42:71–83.
   PubMed Web of Science ®Google Scholar
• Walters WA, Xu Z, Knight R. Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett [Internet] 2014; 588:4223–4233. 10.1016/j.febslet.2014.09.039
   PubMed Web of Science ®Google Scholar
• Png CW, Lindén SK, Gilshenan KS, Zoetendal EG, McSweeney CS, Sly LI, McGuckin MA, Florin THJ. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am J Gastroenterol [Internet] 2010; 105:2420–2428. Available from https://journals.lww.com/00000434-201011000-00018
   PubMed Web of Science ®Google Scholar
• Zuo W, Wang B, Bai X, Luan Y, Fan Y, Michail S, Sun F. 16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis. Sci Rep [Internet] 2022; 12:6421. Available from: https://www.nature.com/articles/s41598-022-07995-7
   PubMed Web of Science ®Google Scholar
• Braden TT, Yixuan H, George MC, Eran S, Aleksandar DK, Chirag JP. The predictive power of the microbiome exceeds that of genome-wide association studies in the discrimination of complex human disease. bioRxiv. [Internet] 2020; Available from. doi:10.1101/2019.12.31.891978.
   Google Scholar
• Schulberg J, De Cruz P. Characterisation and therapeutic manipulation of the gut microbiome in inflammatory bowel disease. Intern Med J [Internet] 2016; 46:266–273. Available from: https://onlinelibrary.wiley.com/doi/10.1111/imj.13003
   PubMed Web of Science ®Google Scholar
• Abt MC, McKenney PT, Pamer EG. Clostridium difficile colitis: pathogenesis and host defence. Nat Rev Microbiol [Internet] 2016; 14:609–620. Available from: http://www.nature.com/articles/nrmicro.2016.108
   PubMed Web of Science ®Google Scholar
• Timms VJ, Daskalopoulos G, Mitchell HM, Neilan BA, Sechi LA. The Association of Mycobacterium avium subsp. paratuberculosis with Inflammatory Bowel Disease. PLoS One [Internet] 2016; 11:e0148731. Available from: https://dx.plos.org/10.1371/journal.pone.0148731
   PubMed Web of Science ®Google Scholar
• Proietti E, Fuhler GM, Peppelenbosch MP. Mycobacterium Avium Subspecies Paratuberculosis Infection and Biological Treatment of IBD: cause or Consequence? J Crohn’s Colitis [Internet] 2021; 15:1247–1249. Available from: https://academic.oup.com/ecco-jcc/article/15/8/1247/6178361
   Google Scholar
• Liu F, Ma R, Tay CYA, Octavia S, Lan R, Chung HKL, Riordan SM, Grimm MC, Leong RW, Tanaka MM, et al. Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn’s disease. Emerg Microbes Infect [Internet] 2018; 7:1–14.
   PubMed Web of Science ®Google Scholar
• Castaño-Rodríguez N, Kaakoush NO, Lee WS, Mitchell HM. Dual role of Helicobacter and Campylobacter species in IBD: a systematic review and meta-analysis. Gut Internet] 2017; 66:235–249. Available from: https://gut.bmj.com/lookup/doi/10.1136/gutjnl-2015-310545
   PubMed Web of Science ®Google Scholar
• Bartonickova L, Sterzenbach T, Nell S, Kops F, Schulze J, Venzke A, Brenneke B, Bader S, Gruber AD, Suerbaum S, et al. Hcp and VgrG1 are secreted components of the Helicobacter hepaticus type VI secretion system and VgrG1 increases the bacterial colitogenic potential. Cell Microbiol [Internet] 2013; 15:992–1011.
   PubMed Web of Science ®Google Scholar
• Yang H, Mirsepasi-Lauridsen HC, Struve C, Allaire JM, Sivignon A, Vogl W, Bosman ES, Ma C, Fotovati A, Reid GS, et al. Ulcerative Colitis-associated E. coli pathobionts potentiate colitis in susceptible hosts. Gut Microbes [Internet] 2020; 12:1847976.
   PubMed Web of Science ®Google Scholar
• Palmela C, Chevarin C, Xu Z, Torres J, Sevrin G, Hirten R, Barnich N, Ng SC, Colombel J-F. Adherent-invasive Escherichia coli in inflammatory bowel disease. Gut [Internet] 2018; 67:574–587. Available from: https://gut.bmj.com/lookup/doi/10.1136/gutjnl-2017-314903
   PubMed Web of Science ®Google Scholar
• Liu JZ, van Sommeren S, Huang H, Ng SC, Alberts R, Takahashi A, Ripke S, Lee JC, Jostins L, Shah T, et al. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat Genet [Internet] 2015; 47:979–986.
   PubMed Web of Science ®Google Scholar
• Furey TS, Sethupathy P, Sheikh SZ. Redefining the IBDs using genome-scale molecular phenotyping. Nat Rev Gastroenterol Hepatol [Internet] 2019; 16:296–311. Available from: http://www.nature.com/articles/s41575-019-0118-x
   PubMed Web of Science ®Google Scholar
• Aschard H, Laville V, Tchetgen ET, Knights D, Imhann F, Seksik P, Zaitlen N, Silverberg MS, Cosnes J, Weersma RK, et al. Genetic effects on the commensal microbiota in inflammatory bowel disease patients. PLOS Genet [Internet] 2019; 15:e1008018.
   PubMed Web of Science ®Google Scholar
• Luo P, Yang Z, Chen B, Zhong X. The multifaceted role of CARD9 in inflammatory bowel disease. J Cell Mol Med [Internet] 2020; 24:34–39. Available from: https://onlinelibrary.wiley.com/doi/10.1111/jcmm.14770
   PubMed Web of Science ®Google Scholar
• Frank DN, St. Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci [Internet] 2007; 104:13780–13785. Available from: https://pnas.org/doi/full/10.1073/pnas.0706625104
   PubMed Web of Science ®Google Scholar
• Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science (80-) [Internet] 2005; 308:1635–1638. Available from: https://www.science.org/doi/10.1126/science.1110591
   PubMed Web of Science ®Google Scholar
• Golińska E, Tomusiak A, Gosiewski T, Więcek G, Machul A, Mikołajczyk D, Bulanda M, Heczko PB, Strus M. Virulence factors of Enterococcus strains isolated from patients with inflammatory bowel disease. World J Gastroenterol [Internet] 2013; 19:3562–3572. Available from: http://www.wjgnet.com/1007-9327/full/v19/i23/3562.htm
   PubMed Web of Science ®Google Scholar
• Ge L, Qi J, Shao B, Ruan Z, Ren Y, Sui S, Wu X, Sun X, Liu S, Li S, et al. Microbial hydrogen economy alleviates colitis by reprogramming colonocyte metabolism and reinforcing intestinal barrier. Gut Microbes [Internet] 2022; 14. Available from: https://www.tandfonline.com/doi/full/10.1080/19490976.2021.2013764
   Web of Science ®Google Scholar
• Selwal KK, Selwal MK, Yu Z. Mucolytic bacteria: prevalence in various pathological diseases. World J Microbiol Biotechnol [Internet] 2021; 37:176.Available from: https://link.springer.com/10.1007/s11274-021-03145-9
   PubMed Web of Science ®Google Scholar
• Yu S, Balasubramanian I, Laubitz D, Tong K, Bandyopadhyay S, Lin X, Flores J, Singh R, Liu Y, Macazana C, et al. Paneth cell-derived lysozyme defines the composition of mucolytic microbiota and the inflammatory tone of the intestine. Immunity [Internet] 2020; 53:398–416.e8.
   PubMed Web of Science ®Google Scholar
• Sokol H, Leducq V, Aschard H, Pham H-P, Jegou S, Landman C, Cohen D, Liguori G, Bourrier A, Nion-Larmurier I, et al. Fungal microbiota dysbiosis in IBD. Gut [Internet] 2017; 66:1039–1048.
   PubMed Web of Science ®Google Scholar
• Liguori G, Lamas B, Richard ML, Brandi G, da Costa G, Hoffmann TW, Di Simone MP, Calabrese C, Poggioli G, Langella P, et al. Fungal dysbiosis in mucosa-associated microbiota of crohn’s disease patients. J Crohn’s Colitis [Internet] 2016; 10:296–305
   Google Scholar
• Clooney AG, Sutton TDS, Shkoporov AN, Holohan RK, Daly KM, O’Regan O, Ryan FJ, Draper LA, Plevy SE, Ross RP, et al. Whole-virome analysis sheds light on viral dark matter in inflammatory bowel disease. Cell Host Microbe [Internet] 2019; 26:764–778.e5
   PubMed Web of Science ®Google Scholar
• Yu M, Jia H, Zhou C, Yang Y, Zhao Y, Yang M, Zou Z. Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics. J Pharm Biomed Anal [Internet] 2017; 138:231–239. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0731708516309384
   PubMed Web of Science ®Google Scholar
• Peng W, Yi P, Yang J, Xu P, Wang Y, Zhang Z, Huang S, Wang Z, Zhang C. Association of gut microbiota composition and function with a senescence-accelerated mouse model of Alzheimer’s Disease using 16S rRNA gene and metagenomic sequencing analysis. Aging (Albany NY) [Internet] 2018; 10:4054–4065. Available from: https://www.aging-us.com/lookup/doi/10.18632/aging.101693
   PubMedGoogle Scholar
• Xu X, Ocansey DKW, Hang S, Wang B, Amoah S, Yi C, Zhang X, Liu L, Mao F. The gut metagenomics and metabolomics signature in patients with inflammatory bowel disease. Gut Pathog [Internet] 2022; 14:26. Available from: https://gutpathogens.biomedcentral.com/articles/10.1186/s13099-022-00499-9
   PubMed 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; 158:930–946.e1. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0016508519418933
   PubMed Web of Science ®Google Scholar
• Kim M, Vogtmann E, Ahlquist DA, Devens ME, Kisiel JB, Taylor WR, White BA, Hale VL, Sung J, Chia N, et al. Fecal metabolomic signatures in colorectal adenoma patients are associated with gut microbiota and early events of colorectal cancer pathogenesis. MBio. 2020; 11(1):e03186–19. doi:10.1128/mBio.03186-19
   PubMed Web of Science ®Google Scholar
• Coker OO, Liu C, Wu WKK, Wong SH, Jia W, Sung JJY, Yu J. Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers. Microbiome [Internet] 2022; 10:35. Available from: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01208-5
   PubMed Web of Science ®Google Scholar
• Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, Carlsson CM, Asthana S, Zetterberg H, Blennow K, et al. Gut microbiome alterations in Alzheimer’s disease. Sci Rep [Internet] 2017; 7:13537.
   PubMedGoogle Scholar
• Yan Z, Yang F, Cao J, Ding W, Yan S, Shi W, Wen S, Yao L. Alterations of gut microbiota and metabolome with Parkinson’s disease. Microb Pathog [Internet] 2021; 160:105187. Available from https://linkinghub.elsevier.com/retrieve/pii/S0882401021004617
   PubMed Web of Science ®Google Scholar
• Yan Q, Gu Y, Li X, Yang W, Jia L, Chen C, Han X, Huang Y, Zhao L, Li P, et al. Alterations of the gut microbiome in hypertension. Front Cell Infect Microbiol Internet] 2017; 7. Available from: http://journal.frontiersin.org/article/10.3389/fcimb.2017.00381/full
   Web of Science ®Google Scholar
• Zhou Z, Zheng Z, Xiong X, Chen X, Peng J, Yao H, Pu J, Chen Q, Zheng M. Gut microbiota composition and fecal metabolic profiling in patients with diabetic retinopathy. Front Cell Dev Biol [Internet] 2021; 9. Available from https://www.frontiersin.org/articles/10.3389/fcell.2021.732204/full.
   Web of Science ®Google Scholar
• Wu GD, Lewis JD, Hoffmann C, Chen -Y-Y, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, et al. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol Internet] 2010; 10(1):206. Available from: https://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-10-206
   PubMed Web of Science ®Google Scholar
• Zmora N, Zilberman-Schapira G, Suez J, Mor U, Dori-Bachash M, Bashiardes S, Kotler E, Zur M, Regev-Lehavi D, Brik RB-Z, et al. Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell Internet] 2018; 174(6):1388–1405.e21. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0092867418311024
   PubMed Web of Science ®Google Scholar
• Ringel Y, Maharshak N, Ringel-Kulka T, Wolber EA, Sartor RB, Carroll IM. High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals. Gut Microbes Internet] 2015; 6:173–181. Available from. ;(3):. http://www.tandfonline.com/doi/full/10.1080/19490976.2015.1044711
   PubMed Web of Science ®Google Scholar
• Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol Internet] 2016; 14:20–32. Available from. ;(1):. https://www.nature.com/articles/nrmicro3552
   PubMed Web of Science ®Google Scholar
• Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, et al. The Treatment-Naive Microbiome in New-Onset Crohn’s Disease. Cell Host Microbe Internet] 2014; 15(3):382–392. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1931312814000638
   PubMed Web of Science ®Google Scholar
• Tropini C, Moss EL, Merrill BD, Ng KM, Higginbottom SK, Casavant EP, Gonzalez CG, Fremin B, Bouley DM, Elias JE, et al. Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota. Cell Internet] 2018; 173(7):1742–1754.e17. Available from:https://linkinghub.elsevier.com/retrieve/pii/S0092867418305853
   PubMed Web of Science ®Google Scholar
• Bucher P, Gervaz P, Egger J-F, Soravia C, Morel P. Morphologic Alterations Associated With Mechanical Bowel Preparation Before Elective Colorectal Surgery: a Randomized Trial. Dis Colon Rectum Internet] 2006; 49:109–112. Available from. ;(1):. https://journals.lww.com/00003453-200649010-00014
   PubMed Web of Science ®Google Scholar
• Tang Q, Jin G, Wang G, Liu T, Liu X, Wang B, Cao H. Current sampling methods for gut microbiota: a call for more precise devices. Front Cell Infect Microbiol [Internet] 2020; 10. Available from: https://www.frontiersin.org/article/10.3389/fcimb.2020.00151/full.
   Web of Science ®Google Scholar
• Jalanka J, Salonen A, Salojärvi J, Ritari J, Immonen O, Marciani L, Gowland P, Hoad C, Garsed K, Lam C, et al. Effects of bowel cleansing on the intestinal microbiota. Gut [Internet] 2015; 64:1562–1568. Available from: https://gut.bmj.com/lookup/doi/10.1136/gutjnl-2014-307240
   PubMed Web of Science ®Google Scholar
• Wensel CR, Pluznick JL, Salzberg SL, Sears CL. Next-generation sequencing: insights to advance clinical investigations of the microbiome. J Clin Invest Internet] 2022; 132. Available from:. ;(7). https://www.jci.org/articles/view/154944
   PubMed Web of Science ®Google Scholar
• Ju F, Zhang T. 16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions. Appl Microbiol Biotechnol [Internet] 2015; 99:4119–4129. Available from: http://link.springer.com/10.1007/s00253-015-6536-y
   PubMed Web of Science ®Google Scholar
• Aldars-García L, Chaparro M, Gisbert JP. Systematic review: the gut microbiome and its potential clinical application in inflammatory bowel disease. Microorganisms Internet] 2021; 9:977. Available from: https://www.mdpi.com/2076-2607/9/5/977
   PubMed Web of Science ®Google Scholar
• Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res [Internet] 2013; 41:e1–e1. Available from https://academic.oup.com/nar/article/41/1/e1/1164457
   PubMed Web of Science ®Google Scholar
• Sanschagrin S, Yergeau E. Next-generation sequencing of 16S ribosomal RNA gene amplicons. J Vis Exp[Internet] 2014; Available from: http://www.jove.com/video/51709/next-generation-sequencing-of-16s-ribosomal-rna-gene-amplicons
   PubMed Web of Science ®Google Scholar
• Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, Hugenholtz P, van der Lelie D, Meyer F, Stevens R, et al. Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol Internet] 2012; 30(6):513–520. Available from: http://www.nature.com/articles/nbt.2235
   PubMed Web of Science ®Google Scholar
• Laudadio I, Fulci V, Palone F, Stronati L, Cucchiara S, Carissimi C. Quantitative assessment of shotgun metagenomics and 16S rDNA amplicon sequencing in the study of human gut microbiome. Omi A J Integr Biol [Internet] 2018; 22:248–254. Available from: http://www.liebertpub.com/doi/10.1089/omi.2018.0013
   PubMed Web of Science ®Google Scholar
• Gasaly N, de Vos P, Hermoso MA. Impact of bacterial metabolites on gut barrier function and host immunity: a focus on bacterial metabolism and its relevance for intestinal inflammation. Front Immunol [Internet] 2021; 12. Available from: https://www.frontiersin.org/articles/10.3389/fimmu.2021.658354/full.
   PubMed Web of Science ®Google Scholar
• van der Giessen J, Binyamin D, Belogolovski A, Frishman S, Tenenbaum-Gavish K, Hadar E, Louzoun Y, Peppelenbosch MP, van der Woude CJ, Koren O, et al. Modulation of cytokine patterns and microbiome during pregnancy in IBD. Gut Internet] 2020; 69:473–86. Available from: https://gut.bmj.com/lookup/doi/10.1136/gutjnl-2019-318263
   Google Scholar
• Sheehan D, Moran C, Shanahan F. The microbiota in inflammatory bowel disease. J Gastroenterol [Internet] 2015; 50:495–507. Available from: http://link.springer.com/10.1007/s00535-015-1064-1
   PubMedGoogle Scholar
• Ma Y, Zhang Y, Jiang H, Xiang S, Zhao Y, Xiao M, Du F, Ji H, Kaboli PJ, Wu X, et al. Metagenome analysis of intestinal bacteria in healthy people, patients with inflammatory bowel disease and colorectal cancer. Front Cell Infect Microbiol [Internet]. 2021; 11. Available from: https://www.frontiersin.org/articles/10.3389/fcimb.2021.599734/full.
   Web of Science ®Google Scholar
• Richard ML, Sokol H. The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases. Nat Rev Gastroenterol Hepatol [Internet] 2019; Available from: http://www.nature.com/articles/s41575-019-0121-2
   PubMed Web of Science ®Google Scholar
• Nishida A, Inoue R, Inatomi O, Bamba S, Naito Y, Andoh A. Gut microbiota in the pathogenesis of inflammatory bowel disease. Clin J Gastroenterol. 2018 [Internet]. 11:1–10. doi:10.1007/s12328-017-0813-5.
   PubMed Web of Science ®Google Scholar
• Kabeerdoss J, Sankaran V, Pugazhendhi S, Ramakrishna BS. Clostridium leptum group bacteria abundance and diversity in the fecal microbiota of patients with inflammatory bowel disease: a case–control study in India. BMC Gastroenterol [Internet] 2013; 13:20. Available from: https://bmcgastroenterol.biomedcentral.com/articles/10.1186/1471-230X-13-20
   PubMed Web of Science ®Google Scholar
• Lopez-Siles M, Martinez-Medina M, Abellà C, Busquets D, Sabat-Mir M, Duncan SH, Aldeguer X, Flint HJ, Garcia-Gil LJ, Elkins CA. Mucosa-associated faecalibacterium prausnitzii phylotype richness is reduced in patients with inflammatory bowel disease. Appl Environ Microbiol [Internet] 2015; 81:7582–92. Available from; https://journals.asm.org/doi/10.1128/AEM.02006-15
   PubMed Web of Science ®Google Scholar
• Lesnik KL, Cai W, Liu H. Microbial community predicts functional stability of microbial fuel cells. Environ Sci Technol [Internet] 2020; 54:427–436. Available from: https://pubs.acs.org/doi/10.1021/acs.est.9b03667
   PubMed Web of Science ®Google Scholar
• Butler S, O’Dwyer JP. Stability criteria for complex microbial communities. Nat Commun [Internet] 2018; 9:2970. Available from: http://www.nature.com/articles/s41467-018-05308-z
   PubMed Web of Science ®Google Scholar
• De Sire R, Talocco C, Petito V, Lopetuso LR, Graziani C, Gasbarrini A, Scaldaferri F. Microbiota and inflammatory bowel disease: an update. Recenti Prog Med [Internet] 2018; 109:570–573. Available from: http://www.ncbi.nlm.nih.gov/pubmed/30667386
   PubMedGoogle Scholar
• Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol [Internet] 2012; 13:R79. Available from: http://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-9-r79
   PubMed Web of Science ®Google Scholar
• Lo Sasso G, Khachatryan L, Kondylis A, Battey JND, Sierro N, Danilova NA, Grigoryeva TV, Markelova MI, Khusnutdinova DR, Laikov AV, et al. Inflammatory Bowel Disease–Associated Changes in the Gut: focus on Kazan Patients. Inflamm Bowel Dis [Internet] 2021; 27:418–433. Available from: https://academic.oup.com/ibdjournal/article/27/3/418/5885057
   PubMedGoogle Scholar
• Forbes JD, Van Domselaar G, Bernstein CN. The gut microbiota in immune-mediated inflammatory diseases. Front Microbiol [Internet] 2016; 7. Available from: http://journal.frontiersin.org/Article/10.3389/fmicb.2016.01081/abstract.
   PubMed Web of Science ®Google Scholar
• Constante M, Fragoso G, Calvé A, Samba-Mondonga M, Santos MM. Dietary heme induces gut dysbiosis, aggravates colitis, and potentiates the development of adenomas in mice. Front Microbiol [Internet] 2017; 8. Available from http://journal.frontiersin.org/article/10.3389/fmicb.2017.01809/full
   PubMed Web of Science ®Google Scholar
• Wiese DM, Horst SN, Brown CT, Allaman MM, Hodges ME, Slaughter JC, Druce JP, Beaulieu DB, Schwartz DA, Wilson KT, et al. Serum fatty acids are correlated with inflammatory cytokines in ulcerative colitis. PLoS One [Internet] 2016; 11:e0156387.
   PubMed Web of Science ®Google Scholar
• Vester-Andersen MK, Mirsepasi-Lauridsen HC, Prosberg MV, Mortensen CO, Träger C, Skovsen K, Thorkilgaard T, Nøjgaard C, Vind I, Krogfelt KA, et al. Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis. Sci Rep [Internet] 2019; 9:13473.
   PubMed Web of Science ®Google Scholar
• Clooney AG, Eckenberger J, Laserna-Mendieta E, Sexton KA, Bernstein MT, Vagianos K, Sargent M, Ryan FJ, Moran C, Sheehan D, et al. Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study. Gut [Internet]. 2021; 70:499–510.
   PubMed Web of Science ®Google Scholar
• Serrano-Gómez G, Mayorga L, Oyarzun I, Roca J, Borruel N, Casellas F, Varela E, Pozuelo M, Machiels K, Guarner F, et al. Dysbiosis and relapse-related microbiome in inflammatory bowel disease: a shotgun metagenomic approach. Comput Struct Biotechnol J. [Internet] 2021; 19:6481–6489.
   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
• Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D’Amato M, Bonfiglio F, McDonald D, Gonzalez A, et al. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol [Internet] 2017; 2:17004.
   PubMed Web of Science ®Google Scholar
• Strauss J, Kaplan GG, Beck PL, Rioux K, Panaccione R, DeVinney R, Lynch T, Allen-Vercoe E. Invasive potential of gut mucosa-derived fusobacterium nucleatum positively correlates with IBD status of the host. Inflamm Bowel Dis [Internet] 2011; 17:1971–1978. Available from: https://academic.oup.com/ibdjournal/article/17/9/1971-1978/4633800
   PubMed Web of Science ®Google Scholar
• Huh J-W, Roh T-Y. Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis. BMC Microbiol [Internet] 2020; 20:208.Available from: https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01887-4
   PubMed Web of Science ®Google Scholar
• Yu T, Guo F, Yu Y, Sun T, Ma D, Han J, Qian Y, Kryczek I, Sun D, Nagarsheth N, et al. Fusobacterium nucleatum promotes chemoresistance to colorectal cancer by modulating autophagy. Cell [Internet] 2017; 170:548–563.e16.
   PubMed Web of Science ®Google Scholar
• Bullman S, Pedamallu CS, Sicinska E, Clancy TE, Zhang X, Cai D, Neuberg D, Huang K, Guevara F, Nelson T, et al. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Science (80-) [Internet] 2017; 358:1443–1448.
   PubMed Web of Science ®Google Scholar
• Machiels K, Joossens M, Sabino J, De Preter V, Arijs I, Eeckhaut V, Ballet V, Claes K, Van Immerseel F, Verbeke K, et al. A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut [Internet] 2014; 63:1275–1283.
   PubMed Web of Science ®Google Scholar
• Knoll RL, Forslund K, Kultima JR, Meyer CU, Kullmer U, Sunagawa S, Bork P, Gehring S. Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis. Am J Physiol Liver Physiol [Internet] 2017; 312:G327–39. Available from: https://www.physiology.org/doi/10.1152/ajpgi.00293.2016
   PubMed Web of Science ®Google Scholar
• Kotlowski R, Bernstein CN, Sepehri S, Krause DO. High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease. Gut [Internet] 2007; 56:669–675. Available from: https://gut.bmj.com/lookup/doi/10.1136/gut.2006.099796
   PubMed Web of Science ®Google Scholar
• Petersen AM, Nielsen EM, Litrup E, Brynskov J, Mirsepasi H, Krogfelt KA. A phylogenetic group of Escherichia coli associated with active left-sided Inflammatory Bowel Disease. BMC Microbiol [Internet] 2009; 9:171. Available from: http://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-9-171
   PubMed Web of Science ®Google Scholar
• Ventin-Holmberg R, Eberl A, Saqib S, Korpela K, Virtanen S, Sipponen T, Salonen A, Saavalainen P, Nissilä E. Bacterial and fungal profiles as markers of infliximab drug response in inflammatory bowel disease. J Crohn’s Colitis [Internet] 2021; 15:1019–1031. Available from: https://academic.oup.com/ecco-jcc/article/15/6/1019/6029424
   Google Scholar
• Pascal V, Pozuelo M, Borruel N, Casellas F, Campos D, Santiago A, Martinez X, Varela E, Sarrabayrouse G, Machiels K, et al. A microbial signature for Crohn’s disease. Gut [Internet] 2017; 66:813–822.
   PubMed Web of Science ®Google Scholar
• Yang Z-H, Liu F, Zhu X-R, Suo F-Y, Jia Z, Yao S-K. Altered profiles of fecal bile acids correlate with gut microbiota and inflammatory responses in patients with ulcerative colitis. World J Gastroenterol [Internet] 2021; 27:3609–3629. Available from: https://www.wjgnet.com/1007-9327/full/v27/i24/3609.htm
   PubMed Web of Science ®Google Scholar
• Mirsepasi-Lauridsen HC, Vallance BA, Krogfelt KA, Petersen AM. Escherichia coli Pathobionts Associated with Inflammatory Bowel Disease. Clin Microbiol Rev [Internet] 2019; 32. Available from: https://journals.asm.org/doi/10.1128/CMR.00060-18
   PubMed Web of Science ®Google Scholar
• Wang L, Christophersen CT, Sorich MJ, Gerber JP, Angley MT, Conlon MA. Increased abundance of Sutterella spp. and Ruminococcus torques in feces of children with autism spectrum disorder. Mol Autism [Internet] 2013; 4:42.Available from: https://molecularautism.biomedcentral.com/articles/10.1186/2040-2392-4-42
   PubMed Web of Science ®Google Scholar
• Pandit L, Cox LM, Malli C, D’Cunha A, Rooney T, Lokhande H, Willocq V, Saxena S, Chitnis T. Clostridium bolteae is elevated in neuromyelitis optica spectrum disorder in India and shares sequence similarity with AQP4. Neurol - Neuroimmunol Neuroinflammation [Internet] 2021; 8:e907. Available from: http://nn.neurology.org/lookup/doi/10.1212/NXI.0000000000000907.
   PubMed Web of Science ®Google Scholar
• Zhou Y, ZZ X, He Y, Yang Y, Liu L, Lin Q, Nie Y, Li M, Zhi F, Liu S, et al. Gut microbiota offers universal biomarkers across ethnicity in inflammatory bowel disease diagnosis and infliximab response prediction. mSystems [Internet] 2018; 3. Available from: https://journals.asm.org/doi/10.1128/mSystems.00188-17.
   Web of Science ®Google Scholar
• Ramanan D, Tang MS, Bowcutt R, Loke P, Cadwell K. Bacterial sensor Nod2 prevents inflammation of the small intestine by restricting the expansion of the commensal bacteroides vulgatus. Immunity [Internet] 2014; 41:311–324. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1074761314002416
   PubMed Web of Science ®Google Scholar
• Chu H, Khosravi A, Kusumawardhani IP, Kwon AHK, Vasconcelos AC, Cunha LD, Mayer AE, Shen Y, Wu W-L, Kambal A, et al. Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Science [Internet] 2016; 352:1116–1120.
   PubMed Web of Science ®Google Scholar
• López EL, Prado-Jiménez V, O’Ryan-Gallardo M, Contrini MM. Shigella and shiga toxin-producing escherichia coli causing bloody diarrhea in Latin America. Infect Dis Clin North Am [Internet] 2000; 14:41–65. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0891552005702178
   PubMed Web of Science ®Google Scholar
• Raisch J. Colon cancer-associated B2 Escherichia coli colonize gut mucosa and promote cell proliferation. World J Gastroenterol Internet] 2014; 20:6560. Available from: http://www.wjgnet.com/1007-9327/full/v20/i21/6560.htm
   PubMed Web of Science ®Google Scholar
• Viljoen KS, Dakshinamurthy A, Goldberg P, Blackburn JM, McDowell A. Quantitative profiling of colorectal cancer-associated bacteria reveals associations between fusobacterium spp., enterotoxigenic bacteroides fragilis (ETBF) and clinicopathological features of colorectal cancer. PLoS One [Internet] 2015; 10:e0119462. Available from: https://dx.plos.org/10.1371/journal.pone.0119462
   PubMed Web of Science ®Google Scholar
• Mima K, Nishihara R, Qian ZR, Cao Y, Sukawa Y, Nowak JA, Yang J, Dou R, Masugi Y, Song M, et al. Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis. Gut [Internet] 2016; 65:1973–1980. Available from https://gut.bmj.com/lookup/doi/10.1136/gutjnl-2015-310101
   PubMed Web of Science ®Google Scholar
• Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, Clancy TE, Chung DC, Lochhead P, Hold GL, et al. Fusobacterium nucleatum Potentiates Intestinal Tumorigenesis and Modulates the Tumor-Immune Microenvironment. Cell Host Microbe. 2013;14(2):207–215. doi:10.1016/j.chom.2013.07.007.
   PubMed Web of Science ®Google Scholar
• Chen Y, Chen Y, Zhang J, Cao P, Su W, Deng Y, Zhan N, Fu X, Huang Y, Dong W. Fusobacterium nucleatum promotes metastasis in colorectal cancer by activating autophagy signaling via the upregulation of CARD3 expression. Theranostics [Internet] 2020; 10:323–339. Available from: http://www.thno.org/v10p0323.htm
   PubMed Web of Science ®Google Scholar
• Hashemi Goradel N, Heidarzadeh S, Jahangiri S, Farhood B, Mortezaee K, Khanlarkhani N, Negahdari B. Fusobacterium nucleatum and colorectal cancer: a mechanistic overview. J Cell Physiol [Internet] 2019; 234:2337–2344. Available from: https://onlinelibrary.wiley.com/doi/10.1002/jcp.27250
   PubMed Web of Science ®Google Scholar
• Chibbar C. The Gut Microbiota in Celiac Disease and probiotics. Nutrients [Internet] 2019; 11:2375. Available from: https://www.mdpi.com/2072-6643/11/10/2375
   PubMed Web of Science ®Google Scholar
• De Palma G, Nadal I, Medina M, Donat E, Ribes-Koninckx C, Calabuig M, Sanz Y. Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children. BMC Microbiol [Internet] 2010; 10:63. Available from: https://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-10-63
   PubMed Web of Science ®Google Scholar
• López-Siles M, Camprubí-Font C, Gómez Del Pulgar EM, Sabat MM, Busquets D, Sanz Y, Martinez-Medina M. Prevalence, abundance, and virulence of adherent-invasive escherichia coli in ulcerative colitis, colorectal cancer, and coeliac disease. Front Immunol [Internet] 2022; 13. Available from: https://www.frontiersin.org/articles/10.3389/fimmu.2022.748839/full
   Google Scholar
• Di Cagno R, De Angelis M, De Pasquale I, Ndagijimana M, Vernocchi P, Ricciuti P, Gagliardi F, Laghi L, Crecchio C, Guerzoni ME, et al. Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization. BMC Microbiol [Internet] 2011; 11:219.
   PubMed Web of Science ®Google Scholar
• Ou G, Hedberg M, Hörstedt P, Baranov V, Forsberg G, Drobni M, Sandström O, Nyunt Wai S, Johansson I, Hammarström M-L, et al. Proximal small intestinal microbiota and identification of rod-shaped bacteria associated with childhood celiac disease. Am J Gastroenterol [Internet] 2009; 104:3058–3067.
   PubMed Web of Science ®Google Scholar
• Wacklin P, Laurikka P, Lindfors K, Collin P, Salmi T, Lähdeaho M-L, Saavalainen P, Mäki M, Mättö J, Kurppa K, et al. Altered duodenal microbiota composition in celiac disease patients suffering from persistent symptoms on a long-term gluten-free diet. Am J Gastroenterol [Internet] 2014; 109:1933–1941.
   PubMed Web of Science ®Google Scholar
• Pecora F, Persico F, Gismondi P, Fornaroli F, Iuliano S, De’Angelis GL, Esposito S. Gut Microbiota in Celiac Disease: is There Any Role for Probiotics? Front Immunol [Internet] 2020; 11. Available from: https://www.frontiersin.org/article/10.3389/fimmu.2020.00957/full.
   PubMed Web of Science ®Google Scholar
• Sta Ana KM, Madriaga J, Espino MP. β-Lactam antibiotics and antibiotic resistance in Asian lakes and rivers: an overview of contamination, sources and detection methods. Environ Pollut [Internet] 2021; 275:116624. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0269749121002025
   PubMed Web of Science ®Google Scholar
• Micenková L, Frankovičová L, Jaborníková I, Bosák J, Dítě P, Šmarda J, Vrba M, Ševčíková A, Kmeťová M, Šmajs D. Escherichia coli isolates from patients with inflammatory bowel disease: exPEC virulence- and colicin-determinants are more frequent compared to healthy controls. Int J Med Microbiol [Internet] 2018; 308:498–504. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1438422117305167
   PubMed Web of Science ®Google Scholar
• Lee JWJ, Plichta D, Hogstrom L, Borren NZ, Lau H, Gregory SM, Tan W, Khalili H, Clish C, Vlamakis H, et al. Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. Cell Host Microbe [Internet] 2021; 29:1294–1304.e4.
   PubMed Web of Science ®Google Scholar
• Sokol H, Brot L, Stefanescu C, Auzolle C, Barnich N, Buisson A, Fumery M, Pariente B, Le Bourhis L, Treton X, et al. Prominence of ileal mucosa-associated microbiota to predict postoperative endoscopic recurrence in Crohn’s disease. Gut [Internet] 2020; 69:462–472.
   PubMed Web of Science ®Google Scholar
• Machiels K, Pozuelo Del Río M, Martinez-De la Torre A, Xie Z, Pascal Andreu V, Sabino J, Santiago A, Campos D, Wolthuis A, D’Hoore A, et al. Early postoperative endoscopic recurrence in crohn’s disease is characterised by distinct microbiota recolonisation. J Crohn’s Colitis [Internet] 2020; 14:1535–1546.
   Google Scholar
• Quévrain E, Maubert MA, Michon C, Chain F, Marquant R, Tailhades J, Miquel S, Carlier L, Bermúdez-Humarán LG, Pigneur B, et al. Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn’s disease. Gut [Internet] 2016; 65:415–425.
   PubMed Web of Science ®Google Scholar
• Zhou L, Zhang M, Wang Y, Dorfman RG, Liu H, Yu T, Chen X, Tang D, Xu L, Yin Y, et al. Faecalibacterium prausnitzii produces butyrate to maintain Th17/Treg balance and to ameliorate colorectal colitis by inhibiting histone deacetylase 1. Inflamm Bowel Dis Internet] 2018; 24:1926–1940.
   PubMed Web of Science ®Google Scholar
• Patterson AM, Mulder IE, Travis AJ, Lan A, Cerf-Bensussan N, Gaboriau-Routhiau V, Garden K, Logan E, Delday MI, Coutts AGP, et al. Human Gut Symbiont Roseburia hominis Promotes and Regulates Innate Immunity. Front Immunol [Internet] 2017; 8. Available from: http://journal.frontiersin.org/article/10.3389/fimmu.2017.01166/full
   Web of Science ®Google Scholar
• Wang X, Xiao Y, Xu X, Guo L, Yu Y, Li N, Xu C. Characteristics of fecal microbiota and machine learning strategy for fecal invasive biomarkers in pediatric inflammatory bowel disease. Front Cell Infect Microbiol [Internet] 2021; 11. Available from: https://www.frontiersin.org/articles/10.3389/fcimb.2021.711884/full.
   Web of Science ®Google Scholar
• Tomaszewski M, Sanders D, Enns R, Gentile L, Cowie S, Nash C, Petrunia D, Mullins P, Hamm J, Azari-Razm N, et al. Risks associated with colonoscopy in a population-based colon screening program: an observational cohort study. C Open [Internet] 2021; 9:E940–7.
   PubMedGoogle Scholar
• Garg R, Singh A, Ahuja KR, Mohan BP, Ravi SJK, Shen B, Kirby DF, Regueiro M. Risks, time trends, and mortality of colonoscopy‐induced perforation in hospitalized patients. J Gastroenterol Hepatol [Internet] 2020; 35:1381–1386. Available from: https://onlinelibrary.wiley.com/doi/10.1111/jgh.14996
   PubMed Web of Science ®Google Scholar
• Altomare A, Putignani L, Del Chierico F, Cocca S, Angeletti S, Ciccozzi M, Tripiciano C, Dalla Piccola B, Cicala M, Guarino MPL. Gut mucosal-associated microbiota better discloses inflammatory bowel disease differential patterns than faecal microbiota. Dig Liver Dis [Internet] 2019; 51:648–656. Available from: https://linkinghub.elsevier.com/retrieve/pii/S159086581831260X
   PubMedGoogle Scholar
• Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, Matot E, Jona G, Harmelin A, Cohen N, et al. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science (80-) [Internet] 2015; 349:1101–1106. Available from: https://www.science.org/doi/10.1126/science.aac4812
   PubMed Web of Science ®Google Scholar
• Gonzalez CG, Mills RH, Zhu Q, Sauceda C, Knight R, Dulai PS, Gonzalez DJ. Location-specific signatures of Crohn’s disease at a multi-omics scale. Microbiome [Internet] 2022; 10:133. Available from: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01331-x
   PubMed Web of Science ®Google Scholar