Clinical trial Nature communications · 2026 Fecal microbiota transplantation for the decolonization of mucosal adherent-invasive Escherichia coli in Crohn's disease: an open-label pilot study. Xu Z, Jiang H, Huang W, et al. Escherichia coli PubMed ↗
Observational Journal of pediatric gastroenterology and nutrition · 2026 Gut microbiome in pediatric acute pancreatitis and Crohn's disease versus irritable bowel syndrome and healthy controls. Santucci NR, Dike CR, Hellmann J, et al. Mediterraneibacter gnavus PubMed ↗
Observational Gut and liver · 2026 Age-Related Microbial Differences in Newly Diagnosed Crohn's Disease Reveal the Distinct Enrichment of Oral-Associated Taxa in Pediatric Patients. Jeong YS, Kim KO, Park YE, et al. [Clostridium] innocuumMediterraneibacter gnavus PubMed ↗
Systematic review BMC gastroenterology · 2026 Specific alterations in the gut microbiome and metabolome across disease locations of Crohn's disease: a systematic review. Huang J, Chen Z, Chen M, et al. Alistipes communisFaecalibacterium prausnitzii PubMed ↗
Review Journal of bacteriology · 2026 Escherichia coli pathobionts and Crohn's disease: varied genetic paths leading to similar phenotypes. Arroyo-Mendoza M, Lorenzi H, Phillips GJ, et al. Escherichia coli PubMed ↗
Clinical trial Nature communications · 2026 Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn's Disease: a first in human trial. Guarino-Vignon P, Louis E, Pham HP, et al. Faecalibacterium prausnitzii PubMed ↗
Observational Inflammatory bowel diseases · 2026 Altered Gut Microbiota in Pediatric Quiescent Crohn's Disease Patients with Iron Deficiency Anemia. Gordon ES, Goc J, Grier A, et al. Alistipes shahiiAnaerobutyricum soehngenii PubMed ↗
Review Gut · 2026 Adherent-invasive Escherichia coli in Crohn's disease: the 25th anniversary. Barnich N, Arthur JC, Buisson A, et al. Escherichia coli PubMed ↗
Observational The oncologist · 2025 Machine learning identifies a distinct microbiota signature in immune checkpoint inhibitor colitis compared with inflammatory bowel disease. Barberio B, Patuzzi I, Bertin L, et al. Bifidobacterium longum PubMed ↗
Randomized trial MicrobiologyOpen · 2025 The Effects of the Crohn's Disease Exclusion Diet (CDED) Alone Versus CDED Plus Partial Enteral Nutrition (PEN) on Gut Microbiome Composition in Pediatric CD Patients. Rohani P, Ansari A, Shaygantabar M, et al. [Clostridium] leptumFaecalibacterium prausnitzii PubMed ↗
Observational BMC gastroenterology · 2025 Unveiling the diagnostic and pro-inflammatory role of crohn's disease: insights from 16 S-guided discovery and species-specific validation. Xu Y, Xie R, Weng Y, et al. Mediterraneibacter gnavus PubMed ↗
Randomized trial Gastroenterology · 2025 Whole Food Diet Induces Remission in Children and Young Adults With Mild to Moderate Crohn's Disease and Is More Tolerable Than Exclusive Enteral Nutrition: A Randomized Controlled Trial. Aharoni-Frutkoff Y, Plotkin L, Pollak D, et al. Mediterraneibacter gnavus PubMed ↗
Observational Inflammatory bowel diseases · 2025 Deep Sequencing of Crohn's Disease Lamina Propria Phagocytes Identifies Pathobionts and Correlates With Pro-Inflammatory Gene Expression. Jacobsen GE, Gonzalez EE, Mendygral P, et al. Escherichia coliMediterraneibacter gnavus PubMed ↗
Randomized trial Journal of dietary supplements · 2025 A Mushroom Based Prebiotic Supplement Pilot Study Among Patients with Crohn's Disease. Leibovitzh H, Fliss Isakov N, Werner L, et al. Parabacteroides distasonis PubMed ↗
Observational United European gastroenterology journal · 2025 Faecalibacterium Diversity in the Gut Microbiome of Crohn's Disease Patients. Mclellan P, Auger S, Goudiaby MT, et al. Faecalibacterium prausnitzii PubMed ↗
Observational Scientific reports · 2025 Fecal microbiota and genetics in pediatric-onset orofacial granulomatosis and Crohn´s disease. Höyhtyä M, Haaramo A, Nikkonen A, et al. Bifidobacterium adolescentisFaecalibacterium prausnitzii PubMed ↗
Observational Journal of Crohn's & colitis · 2025 A pro-inflammatory diet is associated with growth and virulence of Escherichia coli in pediatric Crohn's disease. Breton J, Tu V, Tanes C, et al. Escherichia coli PubMed ↗
Observational Nature communications · 2024 Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease. Akiyama S, Nishijima S, Kojima Y, et al. Enterococcus faeciumEscherichia coli PubMed ↗
Review European journal of gastroenterology & hepatology · 2024 The role of the fecal microbiota in inflammatory bowel disease. Khalaf R, Sciberras M, Ellul P Escherichia coli PubMed ↗
Observational International journal of molecular sciences · 2024 Integrated Analysis of Microbiome and Metabolome Reveals Disease-Specific Profiles in Inflammatory Bowel Diseases and Intestinal Behçet's Disease. Park Y, Ahn JB, Kim DH, et al. Bacteroides fragilis PubMed ↗
Randomized trial Journal of investigative surgery · 2023 Effects of Mesalamine Combined with Live Combined Bifidobacterium, Lactobacillus and Enterococcus Capsules on Intestinal Mucosa Barrier Function and Intestinal Microbiota in Mildly Active Crohn's Disease Patients. Shen M, Shi Y, Ge Z, et al. Bifidobacterium longumPhocaeicola vulgatus PubMed ↗
Review Gastroenterology · 2023 Pathobionts in Inflammatory Bowel Disease: Origins, Underlying Mechanisms, and Implications for Clinical Care. Gilliland A, Chan JJ, De Wolfe TJ, et al. [Clostridium] innocuumPhocaeicola vulgatus PubMed ↗
Observational Annals of clinical microbiology and antimicrobials · 2023 High prevalence of Mucosa-Associated extended-spectrum β-Lactamase-producing Escherichia coli and Klebsiella pneumoniae among Iranain patients with inflammatory bowel disease (IBD). Kharaghani AA, Harzandi N, Khorsand B, et al. Klebsiella pneumoniae PubMed ↗
Review Internal and emergency medicine · 2023 Crohn's disease and breast cancer: a literature review of the mechanisms and treatment. Zhou S, Yu J Bacteroides fragilisMediterraneibacter gnavus PubMed ↗
Review Gut microbes · 2023 The multifaceted virulence of adherent-invasive Escherichia coli. Mansour S, Asrar T, Elhenawy W Escherichia coli PubMed ↗
Observational Microbiome · 2022 Location-specific signatures of Crohn's disease at a multi-omics scale. Gonzalez CG, Mills RH, Zhu Q, et al. Faecalibacterium prausnitziiPhocaeicola vulgatus PubMed ↗
Clinical trial Gut · 2022 Role of adherent and invasive Escherichia coli in Crohn's disease: lessons from the postoperative recurrence model. Buisson A, Sokol H, Hammoudi N, et al. Mediterraneibacter gnavus PubMed ↗
Clinical trial FASEB journal · 2022 Co-occurrence of gut microbiota dysbiosis and bile acid metabolism alteration is associated with psychological disorders in Crohn's disease. Feng L, Zhou N, Li Z, et al. Mediterraneibacter gnavus PubMed ↗
Review Journal of immunology research · 2021 Bifidobacterium Longum: Protection against Inflammatory Bowel Disease. Yao S, Zhao Z, Wang W, et al. Bifidobacterium longum PubMed ↗
Clinical trial Clinical nutrition · 2021 Prebiotic fructans have greater impact on luminal microbiology and CD3+ T cells in healthy siblings than patients with Crohn's disease: A pilot study investigating the potential for primary prevention of inflammatory bowel disease. Hedin CR, McCarthy NE, Louis P, et al. Bifidobacterium adolescentisBifidobacterium longum PubMed ↗
Review Nutrients · 2021 The Modification of the Gut Microbiota via Selected Specific Diets in Patients with Crohn's Disease. Starz E, Wzorek K, Folwarski M, et al. Faecalibacterium prausnitzii PubMed ↗
Observational Scientific reports · 2021 Evaluation of changes in intestinal microbiota in Crohn's disease patients after anti-TNF alpha treatment. Sanchis-Artero L, Martínez-Blanch JF, Manresa-Vera S, et al. Escherichia coliFaecalibacterium prausnitzii PubMed ↗
Observational Journal of gastrointestinal and liver diseases · 2021 Gut microbiota changes in inflammatory bowel diseases and ankylosing spondilytis. Cardoneanu A, Mihai C, Rezus E, et al. [Clostridium] leptumEscherichia coliFaecalibacterium prausnitzii PubMed ↗
Apoptosis · 2026 Microbiota-derived 4-HPAA alleviates Crohn's disease by stabilizing SIRT1 and reprogramming macrophage immunometabolism. Cheng C, Cheng S, Jiang W, et al. Flavonifractor plautii PubMed ↗
Microbial cell factories · 2026 Fecal microbiota fermenting simple organic carbon substrates in vitro as microbial factories capable of distinguishing Crohn's disease from healthy states. Detman-Ignatowska A, Schiro G, Filip R, et al. [Ruminococcus] torquesAgathobacter rectalisCoprococcus catusEscherichia coli +2 more PubMed ↗
PloS one · 2026 Integrative metagenomics and structural bioinformatics identify explainable gut microbial variants associated with Crohn's disease. Khan N, Nasir MM, Aziz U, et al. Agathobacter rectalisBacteroides uniformisPhocaeicola vulgatus PubMed ↗
Clinical and translational gastroenterology · 2026 Phage-Display Immunoprecipitation Sequencing Reveals Distinct Antibody Signatures Against Bacterial Flagellins Associated With Treatment Response in Crohn's Disease. Leibovitzh H, Krongauz D, Schlesinger Y, et al. Roseburia intestinalis PubMed ↗
Biomolecules · 2026 Persistent Gut Microbiota Dysbiosis in Pediatric Crohn's Disease: A Next-Generation Sequencing Pilot Study. Tita GV, Fogas CR, Slavescu KC, et al. Mediterraneibacter gnavus PubMed ↗
Gastroenterology · 2026 β-Glucan and Inulin Estimated Intake Are Associated With Reduced Risk of Crohn's Disease, Improved Gut Barrier and Systemic Inflammation Markers, and Multi-Omic Signatures in a High-Risk Cohort. Xue M, McShane C, Kim J, et al. [Ruminococcus] torques PubMed ↗
Nature communications · 2026 A genetic toolkit for the human gut bacterium Mediterraneibacter gnavus identifies capsular polysaccharides as a competitive colonization factor. Obana N, Nakato G, Nomura N, et al. Mediterraneibacter gnavus PubMed ↗
Frontiers in cellular and infection microbiology · 2026 Colonic biopsy-associated microbial signatures are predictive of response to anti-TNFα biological therapy in Crohn's disease. Zafeiropoulou K, Hageman IL, Mu T, et al. Mediterraneibacter gnavus PubMed ↗
Gastroenterology · 2026 Uncovering the Dynamics of Mucosa-Associated Microbiota in Postoperative Recurrence of Crohn's Disease. Dubois L, Chaussard A, Seksik P, et al. Akkermansia muciniphilaFaecalibacterium prausnitzii PubMed ↗
Cell host & microbe · 2026 Gut DNA virome enterotype dictates inflammation heterogeneity through tuning the phage-bacteria-sphingosine-intestine axis in Crohn's disease. Wen W, Su R, Liu Y, et al. Bacteroides thetaiotaomicronBlautia obeum PubMed ↗
Scientific reports · 2026 Fecal metabolic signals are associated with changes in microbiota and systemic metabolic pathways in Crohn's disease. Levhar N, Hadar R, Braun T, et al. Veillonella disparVeillonella parvula PubMed ↗
Archives of medical research · 2026 Multispecies Signatures and Driving Factors of Oral Microbiome Dysbiosis in Pediatric Crohn's Disease in the United Arab Emirates. Mesto G, Al Atrash E, Rawat D, et al. Veillonella disparVeillonella parvula PubMed ↗
World journal of microbiology & biotechnology · 2025 Comparative metagenomics reveals the differential gut microbiota involved in bile acid metabolism in patients with crohn's disease. Luo S, Li Z, Peng Y, et al. Anaerostipes hadrusCoprococcus catusMediterraneibacter gnavusRoseburia intestinalis PubMed ↗
World journal of gastroenterology · 2025 Combined metabolomic and metagenomic analysis reveals inflammatory bowel disease diversity in pediatric and adult patients. Zakharzhevskaya NB, Erdes SI, Belousova EA, et al. Coprococcus comesStreptococcus salivariusThomasclavelia ramosa PubMed ↗
Nutrients · 2025 Protein-Calorie Malnutrition Is Associated with Altered Colonic Mucosal Microbiota in Inflammatory Bowel Disease. Yang HJ, Corson M, Aja E, et al. [Clostridium] innocuumBifidobacterium longumIntestinibacter bartlettii PubMed ↗
Gut · 2025 Enterococcus faecalis hijacks FABP2 to activate quorum-sensing signals and aggravate Crohn's disease by inducing gut dysbiosis. Sun Y, Huang X, Zhang Y, et al. Enterococcus faecalis PubMed ↗
Journal of translational medicine · 2025 Ruminococcus torques ameliorates the inflammation bowel disease and gut barrier dysfunction by modulating gut microbiota and bile acid metabolism. Lou Y, Lv Y, Wang X, et al. [Ruminococcus] torques PubMed ↗