Role of the gut microbiota in inflammatory bowel disease pathogenesis: what have we learnt in the past 10 years?

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Enhanced Escherichia coli adherence and invasion in Crohn’s disease and colon cancer 1 1The authors thank Professor T. K. Korhonen (Division of General Microbiology, University of Helsinki, Finland), who kindly donated Escherichia coli IH11165; Professor J.-F. Colombel (Laboratoire de Recherche sur les Maladies Inflammatoire de l’Intestine, Centre Hospitalier Universitaire, Lille, France) and Professor A. Darfeuille-Michaud (Faculte de Pharmacie, Clermont-Ferrand, France), who kindly donated the Crohn’s disease ileal isolates LF10 and LF82; and Dr. Keith Leiper (Gastroenterology Unit, Royal Liverpool & Broadgreen University Hospitals Trust, Liverpool, UK) for his cooperation in obtaining colorectal tissue specimens.As a consequence of the work described herein, a patent application has been filed by the University of Liverpool regarding the use of soluble plantain fiber in Crohn’s disease.

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The Crohn’s disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response

Lavoie, S., Conway, K. L., Lassen, K. G., Jijon, H. B., Pan, H., Chun, E., Michaud, M., Lang, J. K., Gallini, C. A., Dreyfuss, J. M., et al. (2019) · eLife · doi:10.7554/elife.39982 · Cited by 153 · see citing works

Microbial protection and virulence in periodontal tissue as a function of polymicrobial communities: symbiosis and dysbiosis

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Giardia Alters Commensal Microbial Diversity throughout the Murine Gut

Barash, N. R., Maloney, J. G., Singer, S. M., & Dawson, S. C. (2017) · Infection and Immunity · doi:10.1128/iai.00948-16 · Cited by 150 · see citing works

Dysbiosis exacerbates colitis by promoting ubiquitination and accumulation of the innate immune adaptor STING in myeloid cells

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Location is important: differentiation between ileal and colonic Crohn’s disease

Atreya, R. N., & Siegmund, B. (2021) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-021-00424-6 · Cited by 146 · see citing works

Green tea extract prevents obesity in male mice by alleviating gut dysbiosis in association with improved intestinal barrier function that limits endotoxin translocation and adipose inflammation

Dey, P., Sasaki, G. Y., Wei, P. Y., Li, J., Wang, L., Zhu, J., McTigue, D. M., Yu, Z., & Bruno, R. S. (2019) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2019.01.017 · Cited by 143 · see citing works

Correlation between early-life regulation of the immune system by microbiota and allergy development

Gensollen, T., & Blumberg, R. S. (2017) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2017.02.011 · Cited by 140 · see citing works

The Role of Probiotics in Nonalcoholic Fatty Liver Disease: A New Insight into Therapeutic Strategies

Meroni, M., Longo, M., & Dongiovanni, P. (2019) · Nutrients · doi:10.3390/nu11112642 · Cited by 146 · see citing works

Characterization of Bacterial and Fungal Microbiome in Children with Hirschsprung Disease with and without a History of Enterocolitis: A Multicenter Study

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Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients

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Importance of gut microbiota in obesity

Cornejo-Pareja, I. M., Muñoz‐Garach, A., Clemente‐Postigo, M., & Tinahones, F. J. (2018) · European Journal of Clinical Nutrition · doi:10.1038/s41430-018-0306-8 · Cited by 138 · see citing works

SIGNR3‐dependent immune regulation by Lactobacillus acidophilus surface layer protein A in colitis

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Mucus Microbiome of Anastomotic Tissue During Surgery Has Predictive Value for Colorectal Anastomotic Leakage

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Saponins regulate intestinal inflammation in colon cancer and IBD

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Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings

Mukherjee, S., Joardar, N., Sengupta, S., & Babu, S. P. S. (2018) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2018.07.010 · Cited by 127 · see citing works

Lactobacillus acidophilus Induces a Strain-specific and Toll-Like Receptor 2–Dependent Enhancement of Intestinal Epithelial Tight Junction Barrier and Protection Against Intestinal Inflammation

Al–Sadi, R., Nighot, P. K., Nighot, M., Haque, M., Rawat, M., & Ma, T. Y. (2021) · American Journal Of Pathology · doi:10.1016/j.ajpath.2021.02.003 · Cited by 124 · see citing works

Gut microbiota‐stem cell niche crosstalk: A new territory for maintaining intestinal homeostasis

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Fecal Microbiota Transplantation for Ulcerative Colitis: A Systematic Review and Meta-Analysis

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Microbiota in cancer development and treatment

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Diet, microbiota, and dysbiosis: a ‘recipe’ for colorectal cancer

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Rifaximin preserves intestinal microbiota balance in patients undergoing allogeneic stem cell transplantation

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Invited Review: From nose to gut – the role of the microbiome in neurological disease

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Association of dietary fibre intake and gut microbiota in adults

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METTL3 overexpression aggravates LPS-induced cellular inflammation in mouse intestinal epithelial cells and DSS-induced IBD in mice

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High Acetate Concentration Protects Intestinal Barrier and Exerts Anti-Inflammatory Effects in Organoid-Derived Epithelial Monolayer Cultures from Patients with Ulcerative Colitis

Deleu, S., Arnauts, K., Deprez, L., Machiels, K., Ferrante, M., Huys, G. R. B., Thevelein, J. M., Raes, J., & Vermeire, S. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24010768 · Cited by 110 · see citing works

Systematic Analysis of the Association between Gut Flora and Obesity through High-Throughput Sequencing and Bioinformatics Approaches

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Factors Determining Colorectal Cancer: The Role of the Intestinal Microbiota

Nistal, E., Fernández-Fernández, N., Vivas, S., & Olcoz, J. L. (2015) · Frontiers in Oncology · doi:10.3389/fonc.2015.00220 · Cited by 107 · see citing works

The role of the gut microbiota in the treatment of inflammatory bowel diseases

Aggeletopoulou, I., Konstantakis, C., Assimakopoulos, S. F., & Triantos, C. K. (2019) · Microbial Pathogenesis · doi:10.1016/j.micpath.2019.103774 · Cited by 101 · see citing works

Critical roles of bile acids in regulating intestinal mucosal immune responses

Sun, R., Xu, C., Feng, B., Gao, X., & Liu, Z. (2021) · Therapeutic Advances in Gastroenterology · doi:10.1177/17562848211018098 · Cited by 99 · see citing works

Patients with Inflammatory Bowel Disease Are at an Increased Risk of Parkinson’s Disease: A South Korean Nationwide Population-Based Study

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Oral iron exacerbates colitis and influences the intestinal microbiome

Mahalhal, A., Williams, J. M., Johnson, S., Ellaby, N., Duckworth, C. A., Burkitt, M. D., Liu, X., Hold, G. L., Campbell, B. J., Pritchard, D. M., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0202460 · Cited by 98 · see citing works

Gut microbiota in health and disease: an overview focused on metabolic inflammation

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Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy

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Gut microbiome-based supervised machine learning for clinical diagnosis of inflammatory bowel diseases

Manandhar, I., Alimadadi, A., Aryal, S., Munroe, P. B., Joe, B., & Cheng, X. (2021) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00360.2020 · Cited by 90 · see citing works

Human Gut Microbiota in Health and Alzheimer’s Disease

Szablewski, L. (2018) · Journal of Alzheimer s Disease · doi:10.3233/jad-170908 · Cited by 92 · see citing works

Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis

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Sexually dimorphic characteristics of the small intestine and colon of prepubescent C57BL/6 mice

Steegenga, W. T., Mischke, M., Lute, C., Boekschoten, M. V., Pruis, M. G. M., Lendvai, Á., Verkade, H. J., Boekhorst, J., Timmerman, H. M., Plösch, T., et al. (2014) · Biology of Sex Differences · doi:10.1186/s13293-014-0011-9 · Cited by 88 · see citing works

Rett Syndrome: A Focus on Gut Microbiota

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Fecal microbiota profiles in treatment-naïve pediatric inflammatory bowel disease – associations with disease phenotype, treatment, and outcome

Olbjørn, C., Småstuen, M. C., Thiis‐Evensen, E., Nakstad, B., Vatn, M. H., Jahnsen, J., Ricanek, P., Vatn, S., Moen, A. E. F., Tannæs, T. M., et al. (2019) · Clinical and Experimental Gastroenterology · doi:10.2147/ceg.s186235 · Cited by 86 · see citing works

Recent advances in clinical practice: a systematic review of isolated colonic Crohn's disease: the third IBD?

Subramanian, S., Ekbom, A., & Rhodes, J. M. (2016) · Gut · doi:10.1136/gutjnl-2016-312673 · Cited by 86 · see citing works

Review article: emerging role of the gut microbiome in the progression of nonalcoholic fatty liver disease and potential therapeutic implications

Jayakumar, S., & Loomba, R. S. (2019) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.15314 · Cited by 88 · see citing works

Prevalence and Phenotype of Concurrent Psoriasis and Inflammatory Bowel Disease

Eppinga, H., Poortinga, S., Thio, H. B., Nijsten, T. E. C., Nuij, V. J. A. A., van der Woude, C. J., Vodegel, R. M., Fuhler, G. M., & Peppelenbosch, M. P. (2017) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000001169 · Cited by 85 · see citing works

Targeting gut barrier dysfunction with phytotherapies: Effective strategy against chronic diseases

Dey, P. (2020) · Pharmacological Research · doi:10.1016/j.phrs.2020.105135 · Cited by 86 · see citing works

Extracts and Marine Algae Polysaccharides in Therapy and Prevention of Inflammatory Diseases of the Intestine

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Serum Metabolomics Identifies Altered Bioenergetics, Signaling Cascades in Parallel with Exposome Markers in Crohn’s Disease

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An evaluation of the effects of probiotics on tumoral necrosis factor (TNF-α) signaling and gene expression

Vincenzi, A., Goettert, M. I., & de Souza, C. F. V. (2020) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2020.10.004 · Cited by 80 · see citing works

Decoding molecular interactions in microbial communities

Abreu, N. A., & Taga, M. E. (2016) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuw019 · Cited by 76 · see citing works

The Research Progress on Intestinal Stem Cells and Its Relationship with Intestinal Microbiota

Hou, Q., Ye, L., Huang, L., & Yu, Q. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00599 · Cited by 79 · see citing works

Cepharanthine ameliorates dextran sulphate sodium‐induced colitis through modulating gut microbiota

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A Transgenic Probiotic Secreting a Parasite Immunomodulator for Site-Directed Treatment of Gut Inflammation

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The role of the Hippo pathway in the pathogenesis of inflammatory bowel disease

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Microbiota in Inflammatory Bowel Disease Pathogenesis and Therapy

Serban, D. E. (2015) · Nutrition in Clinical Practice · doi:10.1177/0884533615606898 · Cited by 77 · see citing works

Ginsenoside Rk3 Ameliorates Obesity-Induced Colitis by Regulating of Intestinal Flora and the TLR4/NF-κB Signaling Pathway in C57BL/6 Mice

Chen, H., Yang, H., Deng, J., & Fan, D. (2021) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.0c07805 · Cited by 74 · see citing works

Unraveling the Role of the Human Gut Microbiome in Health and Diseases

Khalil, M., Ciaula, A. D., Mahdi, L., Jaber, N., Palo, D. M. D., Graziani, A., Baffy, G., & Portincasa, P. (2024) · Microorganisms · doi:10.3390/microorganisms12112333 · Cited by 98 · see citing works

Investigation of Spaceflight Induced Changes to Astronaut Microbiomes

Morrison, M. D., Thissen, J. B., Karouia, F., Mehta, S. K., Urbaniak, C., Venkateswaran, K. J., Smith, D. J., & Jaing, C. J. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.659179 · Cited by 73 · see citing works

The Role of Probiotics in Lipopolysaccharide-Induced Autophagy in Intestinal Epithelial Cells

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Metagenomic analysis of bile salt biotransformation in the human gut microbiome

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Donkey milk consumption exerts anti-inflammatory properties by normalizing antimicrobial peptides levels in Paneth’s cells in a model of ileitis in mice

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Carrageenan Gum and Adherent Invasive Escherichia coli in a Piglet Model of Inflammatory Bowel Disease: Impact on Intestinal Mucosa-associated Microbiota

Munyaka, P. M., Sepehri, S., Ghia, J., & Khafipour, E. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00462 · Cited by 69 · see citing works

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation

Urbaniak, C., Lorenzi, H., Thissen, J. B., Jaing, C. J., Crucian, B. E., Sams, C. F., Pierson, D. L., Venkateswaran, K. J., & Mehta, S. K. (2020) · Microbiome · doi:10.1186/s40168-020-00830-z · Cited by 66 · see citing works

Effects of the Exclusive Enteral Nutrition on the Microbiota Profile of Patients with Crohn’s Disease: A Systematic Review

Gatti, S., Galeazzi, T., Franceschini, E., Annibali, R., Albano, V., Verma, A. K., Angelis, M. D., Lionetti, E., & Catassi, C. (2017) · Nutrients · doi:10.3390/nu9080832 · Cited by 65 · see citing works

The interactions between traditional Chinese medicine and gut microbiota in cancers: Current status and future perspectives

Wei, X., Wang, F., Tan, P., Huang, H., Wang, Z., Xie, J., Wang, L., Liu, D., & Hu, Z. (2024) · Pharmacological Research · doi:10.1016/j.phrs.2024.107148 · Cited by 68 · see citing works

Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome

Kosnicki, K. L., Penprase, J. C., Cintora, P., Torres, P. J., Harris, G. L., Brasser, S. M., & Kelley, S. T. (2018) · Addiction Biology · doi:10.1111/adb.12626 · Cited by 65 · see citing works

Microbiota as Therapeutic Targets

Xavier, R. J. (2016) · Digestive Diseases · doi:10.1159/000445263 · Cited by 16 · see citing works

Microbes in the Pathogenesis of Inflammatory Bowel Disease: A Review

Jatwani, S., Malhotra, B. K., Crout, T. M., & Majithia, V. (2019) · Springer eBooks · doi:10.1007/978-3-030-23311-2_37

Recent progress on the role of gut microbiota in the pathogenesis of inflammatory bowel disease

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Gut bacteriome in inflammatory bowel disease: An update on recent advances

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The gut microbiota and inflammatory bowel disease

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