{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T05:37:13Z","timestamp":1777354633145,"version":"3.51.4"},"reference-count":85,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T00:00:00Z","timestamp":1776729600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Inflammatory bowel diseases (IBDs), including ulcerative colitis (UC) and Crohn\u2019s disease (CD), are consistently associated with alterations in gut microbial communities, although the extent and characteristics of these alterations vary across studies, supporting a potential role of the microbiota in disease pathogenesis and therapeutic modulation. We conducted a systematic review to synthesize current evidence on microbiota alterations in IBD and the clinical application of fecal microbiota transplantation (FMT). A total of 118 studies were included (76 focused on microbiota profiling and 42 evaluated FMT as therapy). Across heterogeneous study designs and microbial characterization methods, reduced microbial diversity was the most consistently reported alteration, generally more pronounced in CD than in UC. Depletion of Faecalibacterium prausnitzii\u2014a key butyrate producer with anti-inflammatory properties\u2014was commonly reported, often accompanied by functional impairment in short-chain fatty acid production. Microbial patterns were frequently associated with mucosal inflammation and varied across disease phenotypes; these patterns have been increasingly explored as predictors of treatment response and relapse, although mechanistic interpretation remains limited and causal relationships are difficult to establish. Evidence from randomized controlled trials suggests potential efficacy of FMT in UC, particularly with intensive or repeated protocols, whereas data in CD remain limited and heterogeneous, with signals of benefit often appearing transient. FMT was generally well tolerated, but long-term safety data remain scarce. Emerging multi-omic approaches are reshaping the field by integrating taxonomic and functional insights, with potential implications for risk stratification, diagnosis, prognosis, and therapeutic optimization. Further standardized, longitudinal, and mechanistically oriented studies are required to translate microbiome research into clinically actionable strategies in IBD.<\/jats:p>","DOI":"10.3390\/pathogens15040451","type":"journal-article","created":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T09:01:24Z","timestamp":1776848484000},"page":"451","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Role of Microbiota and Fecal Transplantation in Inflammatory Bowel Disease"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-7556-1111","authenticated-orcid":false,"given":"Isabel","family":"Lagos","sequence":"first","affiliation":[{"name":"Department of Gastroenterology, Clinica Las Condes, Estoril 450, Santiago 8380453, Chile"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edith","family":"P\u00e9rez de Arce","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, Hospital Clinico Universidad de Chile, Dr. Carlos Lorca Tobar 999, Santiago 8380456, Chile"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-4501-6700","authenticated-orcid":false,"given":"Ilaria","family":"Faggiani","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy, IRCCS San Raffaele Hospital, Via Oglettina 60, 20132 Milan, Italy"},{"name":"Department of Gastroenterology, Vita Salute San Raffaele University, Via Oglettina 60, 21132 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8591-6995","authenticated-orcid":false,"given":"Ferdinando","family":"D\u2019Amico","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy, IRCCS San Raffaele Hospital, Via Oglettina 60, 20132 Milan, Italy"},{"name":"Department of Gastroenterology, Vita Salute San Raffaele University, Via Oglettina 60, 21132 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandra","family":"Zilli","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy, IRCCS San Raffaele Hospital, Via Oglettina 60, 20132 Milan, Italy"},{"name":"Department of Gastroenterology, Vita Salute San Raffaele University, Via Oglettina 60, 21132 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4308-7295","authenticated-orcid":false,"given":"Federica","family":"Furfaro","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy, IRCCS San Raffaele Hospital, Via Oglettina 60, 20132 Milan, Italy"},{"name":"Department of Gastroenterology, Vita Salute San Raffaele University, Via Oglettina 60, 21132 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3214-8192","authenticated-orcid":false,"given":"Sara","family":"Massironi","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy, IRCCS San Raffaele Hospital, Via Oglettina 60, 20132 Milan, Italy"},{"name":"Department of Gastroenterology, Vita Salute San Raffaele University, Via Oglettina 60, 21132 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5400-2765","authenticated-orcid":false,"given":"Clelia","family":"Cicerone","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy, IRCCS San Raffaele Hospital, Via Oglettina 60, 20132 Milan, Italy"},{"name":"Department of Gastroenterology, Vita Salute San Raffaele University, Via Oglettina 60, 21132 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Virginia","family":"Solitano","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy, IRCCS San Raffaele Hospital, Via Oglettina 60, 20132 Milan, Italy"},{"name":"Department of Gastroenterology, Vita Salute San Raffaele University, Via Oglettina 60, 21132 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3398-0231","authenticated-orcid":false,"given":"Tommaso Lorenzo","family":"Parigi","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy, IRCCS San Raffaele Hospital, Via Oglettina 60, 20132 Milan, Italy"},{"name":"Department of Gastroenterology, Vita Salute San Raffaele University, Via Oglettina 60, 21132 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurent","family":"Peyrin-Biroulet","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, INFINY Institute, INSERM NGERE, CHRU Nancy, F-54500 Vandoeuvre-l\u00e8s-Nancy, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvio","family":"Danese","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy, IRCCS San Raffaele Hospital, Via Oglettina 60, 20132 Milan, Italy"},{"name":"Department of Gastroenterology, Vita Salute San Raffaele University, Via Oglettina 60, 21132 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mariangela","family":"Allocca","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy, IRCCS San Raffaele Hospital, Via Oglettina 60, 20132 Milan, Italy"},{"name":"Department of Gastroenterology, Vita Salute San Raffaele University, Via Oglettina 60, 21132 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/nature10209","article-title":"Genetics and Pathogenesis of Inflammatory Bowel Disease","volume":"474","author":"Khor","year":"2011","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/S0016-5085(98)70476-7","article-title":"Early Lesions of Recurrent Crohn\u2019s Disease Caused by Infusion of Intestinal Contents in Excluded Ileum","volume":"114","author":"Geboes","year":"1998","journal-title":"Gastroenterology"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1136\/gutjnl-2020-321106","article-title":"Ranking Microbiome Variance in Inflammatory Bowel Disease: A Large Longitudinal Intercontinental Study","volume":"70","author":"Clooney","year":"2021","journal-title":"Gut"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.1136\/gutjnl-2020-322670","article-title":"Long-Term Dietary Patterns Are Associated with pro-Inflammatory and Anti-Inflammatory Features of the Gut Microbiome","volume":"70","author":"Bolte","year":"2021","journal-title":"Gut"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1053\/j.gastro.2021.03.064","article-title":"Human Microbiota Flagellins Drive Adaptive Immune Responses in Crohn\u2019s Disease","volume":"161","author":"Alexander","year":"2021","journal-title":"Gastroenterology"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1016\/j.cgh.2020.03.013","article-title":"Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases","volume":"19","author":"Borren","year":"2021","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1002\/ibd.20903","article-title":"Low Counts of Faecalibacterium Prausnitzii in Colitis Microbiota","volume":"15","author":"Sokol","year":"2009","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"101624","DOI":"10.1016\/j.xcrm.2024.101624","article-title":"Enhanced Microbiota Profiling in Patients with Quiescent Crohn\u2019s Disease through Comparison with Paired Healthy First-Degree Relatives","volume":"5","author":"Chen","year":"2024","journal-title":"Cell Rep. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.dld.2025.11.014","article-title":"Impact of Oral Butyrate on Clinical and Biochemical Parameters in IBD: A Randomized Placebo-Controlled Study Targeting Gut Microbiota","volume":"58","author":"Facchin","year":"2026","journal-title":"Dig. Liver Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/j.jcmgh.2019.11.012","article-title":"Analysis of Flagellin-Specific Adaptive Immunity Reveals Links to Dysbiosis in Patients with Inflammatory Bowel Disease","volume":"9","author":"Cook","year":"2020","journal-title":"Cell. Mol. Gastroenterol. Hepatol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2112","DOI":"10.1093\/ibd\/izae291","article-title":"Safety and Efficacy of Fecal Microbiota, Live-Jslm (REBYOTA\u00ae), for the Prevention of Recurrent Clostridioides difficile Infection in Participants with Inflammatory Bowel Disease in PUNCH CD3-OLS","volume":"31","author":"Allegretti","year":"2025","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1642","DOI":"10.1136\/gutjnl-2023-329948","article-title":"The First International Rome Consensus Conference on Gut Microbiota and Faecal Microbiota Transplantation in Inflammatory Bowel Disease","volume":"72","author":"Lopetuso","year":"2023","journal-title":"Gut"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Boicean, A., Birlutiu, V., Ichim, C., Anderco, P., and Birsan, S. (2023). Fecal Microbiota Transplantation in Inflammatory Bowel Disease. Biomedicines, 11.","DOI":"10.3390\/biomedicines11041016"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1056\/NEJMoa1205037","article-title":"Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile","volume":"368","author":"Vrieze","year":"2013","journal-title":"N. Engl. J. Med."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1093\/ecco-jcc\/jjae066","article-title":"The Effect of Non-Pooled Multidonor Faecal Microbiota Transplantation for Inducing Clinical Remission in Patients with Chronic Pouchitis: Results from a Multicentre, Randomised, Double-Blinded, Placebo-Controlled Trial [MicroPouch]","volume":"18","author":"Kousgaard","year":"2024","journal-title":"J. Crohns Colitis"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1016\/S0140-6736(17)30182-4","article-title":"Multidonor Intensive Faecal Microbiota Transplantation for Active Ulcerative Colitis: A Randomised Placebo-Controlled Trial","volume":"389","author":"Paramsothy","year":"2017","journal-title":"Lancet"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1001\/jama.2018.20046","article-title":"Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients with Ulcerative Colitis: A Randomized Clinical Trial","volume":"321","author":"Costello","year":"2019","journal-title":"JAMA"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"4753","DOI":"10.1038\/s41598-017-04984-z","article-title":"Multiple Fresh Fecal Microbiota Transplants Induces and Maintains Clinical Remission in Crohn\u2019s Disease Complicated with Inflammatory Mass","volume":"7","author":"He","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1093\/ecco-jcc\/jjae043","article-title":"Faecal Microbiota Transplantation Engraftment After Budesonide or Placebo in Patients with Active Ulcerative Colitis Using Pre-Selected Donors: A Randomized Pilot Study","volume":"18","author":"Nooij","year":"2024","journal-title":"J. Crohns Colitis"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2402","DOI":"10.1097\/MIB.0000000000000908","article-title":"Fecal Microbiota Transplantation Is Safe and Efficacious for Recurrent or Refractory Clostridium Difficile Infection in Patients with Inflammatory Bowel Disease","volume":"22","author":"Fischer","year":"2016","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"100707","DOI":"10.1016\/j.medj.2025.100707","article-title":"Donor Composition and Fiber Promote Strain Engraftment in a Randomized Controlled Trial of Fecal Microbiota Transplant for Ulcerative Colitis","volume":"6","author":"Gogokhia","year":"2025","journal-title":"Med"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/S2468-1253(21)00400-3","article-title":"Lyophilised Oral Faecal Microbiota Transplantation for Ulcerative Colitis (LOTUS): A Randomised, Double-Blind, Placebo-Controlled Trial","volume":"7","author":"Haifer","year":"2022","journal-title":"Lancet Gastroenterol. Hepatol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"n71","DOI":"10.1136\/bmj.n71","article-title":"The PRISMA 2020 Statement: An Updated Guideline for Reporting Systematic Reviews","volume":"372","author":"Page","year":"2021","journal-title":"BMJ"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e22100","DOI":"10.1096\/fj.202101088RRR","article-title":"Co-occurrence of Gut Microbiota Dysbiosis and Bile Acid Metabolism Alteration Is Associated with Psychological Disorders in Crohn\u2019s Disease","volume":"36","author":"Feng","year":"2022","journal-title":"FASEB J."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Walker, A.W., Sanderson, J.D., Churcher, C., Parkes, G.C., Hudspith, B.N., Rayment, N., Brostoff, J., Parkhill, J., Dougan, G., and Petrovska, L. (2011). High-Throughput Clone Library Analysis of the Mucosa-Associated Microbiota Reveals Dysbiosis and Differences between Inflamed and Non-Inflamed Regions of the Intestine in Inflammatory Bowel Disease. BMC Microbiol., 11.","DOI":"10.1186\/1471-2180-11-7"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1844","DOI":"10.1053\/j.gastro.2010.08.049","article-title":"A Pyrosequencing Study in Twins Shows that Gastrointestinal Microbial Profiles Vary with Inflammatory Bowel Disease Phenotypes","volume":"139","author":"Willing","year":"2010","journal-title":"Gastroenterology"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1002\/ibd.20783","article-title":"Twin Studies Reveal Specific Imbalances in the Mucosa-Associated Microbiota of Patients with Ileal Crohn\u02bcs Disease","volume":"15","author":"Willing","year":"2009","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1097\/MIB.0000000000000662","article-title":"Distinct Microbiotas Are Associated with Ileum-Restricted and Colon-Involving Crohn\u2019s Disease","volume":"22","author":"Naftali","year":"2016","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1097\/MIB.0000000000000674","article-title":"Microbiome Heterogeneity Characterizing Intestinal Tissue and Inflammatory Bowel Disease Phenotype","volume":"22","author":"Tyler","year":"2016","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1038\/nrgastro.2017.88","article-title":"Gut Microbiota and IBD: Causation or Correlation?","volume":"14","author":"Ni","year":"2017","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1136\/gut.2005.073817","article-title":"Reduced Diversity of Faecal Microbiota in Crohn\u2019s Disease Revealed by a Metagenomic Approach","volume":"55","author":"Manichanh","year":"2006","journal-title":"Gut"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1080\/00365520802433231","article-title":"Diversity of Mucosa-Associated Microbiota in Active and Inactive Ulcerative Colitis","volume":"44","author":"Nishikawa","year":"2009","journal-title":"Scand. J. Gastroenterol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1111\/jgh.15232","article-title":"Gut Microbiome Diversity in Acute Severe Colitis Is Distinct from Mild to Moderate Ulcerative Colitis","volume":"36","author":"Kedia","year":"2021","journal-title":"J. Gastroenterol. Hepatol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1136\/gutjnl-2019-318719","article-title":"Prominence of Ileal Mucosa-Associated Microbiota to Predict Postoperative Endoscopic Recurrence in Crohn\u2019s Disease","volume":"69","author":"Sokol","year":"2020","journal-title":"Gut"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2078620","DOI":"10.1080\/19490976.2022.2078620","article-title":"Fecal Microbiota and Bile Acids in IBD Patients Undergoing Screening for Colorectal Cancer","volume":"14","author":"Lavelle","year":"2022","journal-title":"Gut Microbes"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1136\/gutjnl-2012-302578","article-title":"Connecting Dysbiosis, Bile-Acid Dysmetabolism and Gut Inflammation in Inflammatory Bowel Diseases","volume":"62","author":"Duboc","year":"2013","journal-title":"Gut"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1111\/jgh.12694","article-title":"Association between Specific Mucosa-associated Microbiota in Crohn\u2019s Disease at the Time of Resection and Subsequent Disease Recurrence: A Pilot Study","volume":"30","author":"Kang","year":"2015","journal-title":"J. Gastroenterol. Hepatol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1713","DOI":"10.1080\/19490976.2020.1778262","article-title":"Luminal Microbiota Related to Crohn\u2019s Disease Recurrence after Surgery","volume":"11","author":"Hamilton","year":"2020","journal-title":"Gut Microbes"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1136\/gutjnl-2013-304833","article-title":"A Decrease of the Butyrate-Producing Species Roseburia hominis and Faecalibacterium prausnitzii Defines Dysbiosis in Patients with Ulcerative Colitis","volume":"63","author":"Machiels","year":"2014","journal-title":"Gut"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"4548","DOI":"10.3748\/wjg.v23.i25.4548","article-title":"Distinct Gut Microbiota Profiles in Patients with Primary Sclerosing Cholangitis and Ulcerative Colitis","volume":"23","author":"Bajer","year":"2017","journal-title":"World J. Gastroenterol."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Quraishi, M.N., Moakes, C.A., Yalchin, M., Segal, J., Ives, N.J., Magill, L., Manzoor, S.E., Gerasimidis, K., Loi, S., and McMullan, C. (2024). Determining the Optimal Route of Faecal Microbiota Transplant in Patients with Ulcerative Colitis: The STOP-Colitis Pilot RCT. Effic. Mech. Eval., 11.","DOI":"10.3310\/YCJD4579"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1136\/gutjnl-2015-310746","article-title":"Fungal Microbiota Dysbiosis in IBD","volume":"66","author":"Sokol","year":"2017","journal-title":"Gut"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"R79","DOI":"10.1186\/gb-2012-13-9-r79","article-title":"Dysfunction of the Intestinal Microbiome in Inflammatory Bowel Disease and Treatment","volume":"13","author":"Morgan","year":"2012","journal-title":"Genome Biol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41564-018-0306-4","article-title":"Gut Microbiome Structure and Metabolic Activity in Inflammatory Bowel Disease","volume":"4","author":"Franzosa","year":"2018","journal-title":"Nat. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"3247","DOI":"10.1093\/ibd\/izaf147","article-title":"Isolated Anastomotic Ulcers Are Associated with a Higher Long-Term Risk for Postoperative Recurrence and a Differential Mucosa-Associated Microbiome Composition in Patients with Crohn\u2019s Disease Following Ileocolic Resection","volume":"31","author":"Bak","year":"2025","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1136\/gutjnl-2017-314903","article-title":"Adherent-Invasive Escherichia coli in Inflammatory Bowel Disease","volume":"67","author":"Palmela","year":"2018","journal-title":"Gut"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1053\/j.gastro.2004.04.061","article-title":"High Prevalence of Adherent-Invasive Escherichia coli Associated with Ileal Mucosa in Crohn\u2019s Disease","volume":"127","author":"Boudeau","year":"2004","journal-title":"Gastroenterology"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s13073-017-0490-5","article-title":"A Novel Ruminococcus Gnavus Clade Enriched in Inflammatory Bowel Disease Patients","volume":"9","author":"Hall","year":"2017","journal-title":"Genome Med."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1970","DOI":"10.1053\/j.gastro.2021.01.030","article-title":"Healthy Cotwins Share Gut Microbiome Signatures With Their Inflammatory Bowel Disease Twins and Unrelated Patients","volume":"160","author":"Brand","year":"2021","journal-title":"Gastroenterology"},{"key":"ref_50","first-page":"978","article-title":"Alterations in the Intestinal Microbiome (Dysbiosis) as a Predictor of Relapse After Infliximab Withdrawal in Crohn\u02bcs Disease","volume":"20","author":"Rajca","year":"2014","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1038\/ismej.2008.37","article-title":"Molecular Analysis of the Gut Microbiota of Identical Twins with Crohn\u2019s Disease","volume":"2","author":"Dicksved","year":"2008","journal-title":"ISME J."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1093\/ibd\/izy085","article-title":"Determinants of IBD Heritability: Genes, Bugs, and More","volume":"24","author":"Turpin","year":"2018","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1136\/gutjnl-2014-308896","article-title":"Siblings of Patients with Crohn\u2019s Disease Exhibit a Biologically Relevant Dysbiosis in Mucosal Microbial Metacommunities","volume":"65","author":"Hedin","year":"2016","journal-title":"Gut"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1136\/gutjnl-2016-312135","article-title":"Interplay of Host Genetics and Gut Microbiota Underlying the Onset and Clinical Presentation of Inflammatory Bowel Disease","volume":"67","author":"Imhann","year":"2018","journal-title":"Gut"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1007\/s00535-010-0368-4","article-title":"Comparison of the Fecal Microbiota Profiles between Ulcerative Colitis and Crohn\u2019s Disease Using Terminal Restriction Fragment Length Polymorphism Analysis","volume":"46","author":"Andoh","year":"2011","journal-title":"J. Gastroenterol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1326","DOI":"10.1093\/ecco-jcc\/jjab020","article-title":"The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease","volume":"15","author":"Ruigrok","year":"2021","journal-title":"J. Crohns Colitis"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"e02120-17","DOI":"10.1128\/mBio.02120-17","article-title":"Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn\u2019s Disease Patients","volume":"9","author":"Doherty","year":"2018","journal-title":"mBio"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1093\/ecco-jcc\/jjae084","article-title":"Gardenia Study Group Gut Microbial Species and Endotypes Associate with Remission in Ulcerative Colitis Patients Treated with Anti-TNF or Anti-Integrin Therapy","volume":"18","author":"Tamburini","year":"2024","journal-title":"J. Crohns Colitis"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.chom.2017.04.010","article-title":"Gut Microbiome Function Predicts Response to Anti-Integrin Biologic Therapy in Inflammatory Bowel Diseases","volume":"21","author":"Ananthakrishnan","year":"2017","journal-title":"Cell Host Microbe"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1097\/MIB.0000000000001130","article-title":"The Mucosal Antibacterial Response Profile and Fecal Microbiota Composition Are Linked to the Disease Course in Patients with Newly Diagnosed Ulcerative Colitis","volume":"23","author":"Magnusson","year":"2017","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"8979","DOI":"10.1038\/s41467-024-53454-4","article-title":"The Phageome of Patients with Ulcerative Colitis Treated with Donor Fecal Microbiota Reveals Markers Associated with Disease Remission","volume":"15","author":"Majzoub","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1093\/ecco-jcc\/jjv209","article-title":"Fungal Dysbiosis in Mucosa-Associated Microbiota of Crohn\u2019s Disease Patients","volume":"10","author":"Liguori","year":"2016","journal-title":"J. Crohns Colitis"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"79","DOI":"10.3109\/09637486.2013.825700","article-title":"In Vitro Batch Cultures of Gut Microbiota from Healthy and Ulcerative Colitis (UC) Subjects Suggest That Sulphate-Reducing Bacteria Levels Are Raised in UC and by a Protein-Rich Diet","volume":"65","author":"Khalil","year":"2014","journal-title":"Int. J. Food Sci. Nutr."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"e13914","DOI":"10.1111\/nmo.13914","article-title":"Microbiota Changes Induced by Microencapsulated Sodium Butyrate in Patients with Inflammatory Bowel Disease","volume":"32","author":"Facchin","year":"2020","journal-title":"Neurogastroenterol. Motil."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.cmet.2016.05.005","article-title":"Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism","volume":"24","author":"Sayin","year":"2016","journal-title":"Cell Metab."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1053\/j.gastro.2015.04.001","article-title":"Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial","volume":"149","author":"Moayyedi","year":"2015","journal-title":"Gastroenterology"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1053\/j.gastro.2015.03.045","article-title":"Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis","volume":"149","author":"Rossen","year":"2015","journal-title":"Gastroenterology"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1038\/ismej.2014.13","article-title":"Reset of a Critically Disturbed Microbial Ecosystem: Faecal Transplant in Recurrent Clostridium difficile Infection","volume":"8","author":"Fuentes","year":"2014","journal-title":"ISME J."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1177\/1756283X12453637","article-title":"Fecal Microbiota Transplantation in Relapsing Clostridium difficile Infection","volume":"5","author":"Rohlke","year":"2012","journal-title":"Ther. Adv. Gastroenterol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1111\/1751-2980.12938","article-title":"Efficacy and Safety of Fecal Microbiota Transplantation by Washed Preparation in Patients with Moderate to Severely Active Ulcerative Colitis","volume":"21","author":"Chen","year":"2020","journal-title":"J. Dig. Dis."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.3748\/wjg.v29.i17.2666","article-title":"Fecal Microbiota Transplantation for the Maintenance of Remission in Patients with Ulcerative Colitis: A Randomized Controlled Trial","volume":"29","author":"Lahtinen","year":"2023","journal-title":"World J. Gastroenterol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"5517","DOI":"10.1038\/s41598-022-09307-5","article-title":"Strain-Resolved Analysis in a Randomized Trial of Antibiotic Pretreatment and Maintenance Dose Delivery Mode with Fecal Microbiota Transplant for Ulcerative Colitis","volume":"12","author":"Smith","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"1982","DOI":"10.1053\/j.gastro.2020.07.045","article-title":"Outcomes of Fecal Microbiota Transplantation in Patients With Inflammatory Bowel Diseases and Recurrent Clostridioides difficile Infection","volume":"159","author":"Allegretti","year":"2020","journal-title":"Gastroenterology"},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Damman, C.J., Brittnacher, M.J., Westerhoff, M., Hayden, H.S., Radey, M., Hager, K.R., Marquis, S.R., Miller, S.I., and Zisman, T.L. (2015). Low Level Engraftment and Improvement Following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0133925"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1334","DOI":"10.14309\/ajg.0000000000003196","article-title":"Preliminary Results From a Multicenter, Randomized Trial Using Fecal Microbiota Transplantation to Induce Remission in Patients with Mild-to-Moderate Crohn\u2019s Disease","volume":"120","author":"Kao","year":"2025","journal-title":"Am. J. Gastroenterol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s40168-020-0792-5","article-title":"Fecal Microbiota Transplantation to Maintain Remission in Crohn\u2019s Disease: A Pilot Randomized Controlled Study","volume":"8","author":"Sokol","year":"2020","journal-title":"Microbiome"},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Tkach, S., Dorofeyev, A., Kuzenko, I., Falalyeyeva, T., Tsyryuk, O., Kovalchuk, O., Kobyliak, N., Abenavoli, L., and Boccuto, L. (2023). Efficacy and Safety of Fecal Microbiota Transplantation via Colonoscopy as Add-on Therapy in Patients with Mild-to-Moderate Ulcerative Colitis: A Randomized Clinical Trial. Front. Med., 9.","DOI":"10.3389\/fmed.2022.1049849"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"2401","DOI":"10.1136\/gutjnl-2022-327811","article-title":"Faecal Microbiota Transplantation with Anti-Inflammatory Diet (FMT-AID) Followed by Anti-Inflammatory Diet Alone Is Effective in Inducing and Maintaining Remission over 1 Year in Mild to Moderate Ulcerative Colitis: A Randomised Controlled Trial","volume":"71","author":"Kedia","year":"2022","journal-title":"Gut"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1186\/s12967-015-0646-2","article-title":"Step-up Fecal Microbiota Transplantation Strategy: A Pilot Study for Steroid-Dependent Ulcerative Colitis","volume":"13","author":"Cui","year":"2015","journal-title":"J. Transl. Med."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1007\/s00253-018-9447-x","article-title":"Timing for the Second Fecal Microbiota Transplantation to Maintain the Long-Term Benefit from the First Treatment for Crohn\u2019s Disease","volume":"103","author":"Li","year":"2019","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1935","DOI":"10.1007\/s12325-018-0800-3","article-title":"The Safety of Fecal Microbiota Transplantation for Crohn\u2019s Disease: Findings from A Long-Term Study","volume":"35","author":"Wang","year":"2018","journal-title":"Adv. Ther."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1053\/j.gastro.2025.09.014","article-title":"The Gut Microbiome at the Onset of Inflammatory Bowel Disease: A Systematic Review and Unified Bioinformatic Synthesis","volume":"170","author":"Rimmer","year":"2026","journal-title":"Gastroenterology"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"3555","DOI":"10.1038\/s41591-024-03280-4","article-title":"Noninvasive, Microbiome-Based Diagnosis of Inflammatory Bowel Disease","volume":"30","author":"Zheng","year":"2024","journal-title":"Nat. Med."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"2182","DOI":"10.1097\/MIB.0000000000000893","article-title":"Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn\u2019s Disease","volume":"22","author":"Vaughn","year":"2016","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"199","DOI":"10.5009\/gnl250360","article-title":"Translating Gut Microbiota into Diagnostics: A Multidimensional Approach for the Diagnosis of Inflammatory Bowel Disease","volume":"20","author":"Lee","year":"2025","journal-title":"Gut Liver"}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/4\/451\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T04:40:03Z","timestamp":1777351203000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/4\/451"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,21]]},"references-count":85,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2026,4]]}},"alternative-id":["pathogens15040451"],"URL":"https:\/\/doi.org\/10.3390\/pathogens15040451","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,21]]}}}