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Cells
Special Issues
Gut Microbiota, Metabolites, and Immune Regulation in Gastrointestinal Diseases
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Gut Microbiota, Metabolites, and Immune Regulation in Gastrointestinal Diseases

A special issue of Cells (ISSN 2073-4409).

Deadline for manuscript submissions: 31 August 2026 | Viewed by 3253

Special Issue Editors

Dr. Sweta Ghosh

E-Mail Website
Guest Editor
Department of Microbiology and Immunology, Brown Cancer Center, Center for Microbiomics, Inflammation and Pathogenicity, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
Interests: immunology; cancer biology; inflammation; stem cell biology; infection immunology
Dr. Subir Kumar Juin

E-Mail Website
Guest Editor
Department of Microbiology and Immunology, University of Louisville School of Medicine, 505 S. Hancock St., Louisville, KY 40202, USA
Interests: cancer immunology; renovascular physiology; neuroinflammation; infectious diseases; endocrine biochemistry

Special Issue Information

Dear Colleagues,

In recent years, gut microbiota and microbial metabolites have emerged as regulators of gastro-intestinal (GI) diseases. The gut microbiota and its metabolites play a critical role in immune regulation, influencing both local and systemic immune responses in the GI tract and beyond. In GI diseases, an imbalanced microbiome (dysbiosis) disrupts this delicate equilibrium, contributing to chronic inflammation and disease progression. Inflammatory Bowel Disease (IBD), Irritable Bowel Syndrome (IBS), and colorectal cancer (CRC) are among the several GI disorders that arise because of immune homeostasis being altered by microbial dysbiosis and changed metabolites. Gut barrier dysfunction, chronic inflammation and susceptibility to other diseases are major concerns for GI diseases. Therapeutic strategies targeting or manipulating the gut microbiota and its metabolites represent a promising avenue for novel GI disease therapies. This Special Issue welcomes manuscripts focusing on any aspect of gut microbiota, metabolite and immunoregulations related to GI diseases.

Dr. Sweta Ghosh
Dr. Subir Kumar Juin
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • gut microbiota
  • microbial metabolites
  • inflammation
  • immunology
  • gut-barrier
  • gastrointestinal disease

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Published Papers (2 papers)

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Review

17 pages, 730 KB  
Review
Exploring the Muco-Microbiotic Interface as a Hub for Microbial Metabolites and Immune Regulation in Gastroenteric Health and Disease
by Adelaide Carista, Melania Ionelia Gratie, Enrico Tornatore, Salvatore Accomando, Giovanni Tomasello, Domiziana Picone, Stefano Burgio and Francesco Cappello
Cells 2026, 15(1), 45; https://doi.org/10.3390/cells15010045 - 25 Dec 2025
Cited by 2 | Viewed by 1021
Abstract
The mucus layer covering the gastrointestinal tract forms a specialised interface where mucins, microbes, and extracellular vesicles create a dynamic, self-regulating ecosystem. Here, we introduce the concept of the muco-microbiotic layer as an integrated eco-physiological system that maintains mucosal homeostasis through coordinated structural, [...] Read more.
The mucus layer covering the gastrointestinal tract forms a specialised interface where mucins, microbes, and extracellular vesicles create a dynamic, self-regulating ecosystem. Here, we introduce the concept of the muco-microbiotic layer as an integrated eco-physiological system that maintains mucosal homeostasis through coordinated structural, metabolic, and immune functions. The MuMi layer varies regionally in its biochemical composition, microbial inhabitants, and environmental parameters—from the acidic stomach to the anaerobic colon—thereby generating distinct niches for microbial colonisation and metabolite production. We summarise current evidence on how mucin glycans, mucus-associated microbiota, and vesicle-mediated signalling sustain barrier integrity, nutrient flux, and immune tolerance. Perturbations in any of these components lead to barrier failure, microbial encroachment, and inflammation, contributing to a broad spectrum of disorders, including gastritis, inflammatory bowel disease, colorectal cancer, and metabolic syndrome. Methodological advances such as organoid and mucus-on-chip models, spatial multi-omics, and vesiculomics are now enabling site-specific analyses of this complex system. Conceptually, defining the mucus, microbiota, and vesicular compartments as a single MuMi layer provides a new framework for understanding mucosal physiology and pathophysiology, emphasising the interdependence between structure and function. Integrating this perspective into experimental and clinical research may open new avenues for diagnostics and therapies targeting mucosal health. Full article
(This article belongs to the Special Issue Gut Microbiota, Metabolites, and Immune Regulation in Gastrointestinal Diseases)
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30 pages, 1801 KB  
Review
Microbiota-Mediated Bile Acid Metabolism as a Mechanistic Framework for Precision Nutrition in Gastrointestinal and Metabolic Diseases
by Suna Kang, Do-Youn Jeong, Jeowon Seo, James W. Daily and Sunmin Park
Cells 2026, 15(1), 23; https://doi.org/10.3390/cells15010023 - 22 Dec 2025
Cited by 4 | Viewed by 1797
Abstract
Gut microbiota play a central role in shaping bile acid (BA) metabolism through community-specific capacities for deconjugation, dehydroxylation, and other transformation reactions. Distinct microbiome compositional patterns—often referred to as enterotype-like clusters—correspond to reproducible functional profiles that generate unique BA metabolic signatures with relevance [...] Read more.
Gut microbiota play a central role in shaping bile acid (BA) metabolism through community-specific capacities for deconjugation, dehydroxylation, and other transformation reactions. Distinct microbiome compositional patterns—often referred to as enterotype-like clusters—correspond to reproducible functional profiles that generate unique BA metabolic signatures with relevance for metabolic and gastrointestinal health. This narrative review synthesizes current evidence describing the interplay between microbial composition, BA metabolism, and metabolic dysfunction. A structured literature search was conducted in PubMed, Web of Science, EMBASE, and Scopus using predefined keywords related to bile acids, microbiome composition, metabolic disorders, and enterotypes. Studies were screened for human clinical relevance and mechanistic insights into BA–microbiome interactions. Across the evidence base, Bacteroides-, Prevotella-, and Ruminococcus-associated community types consistently demonstrate different BA transformation capacities that influence secondary BA production and downstream host signaling through FXR and TGR5. These differences are linked to variation in metabolic dysfunction-associated steatotic liver disease, obesity, type 2 diabetes, inflammatory bowel disease, and colorectal cancer. Host genetic variations in BA synthesis, transport, and signaling further modify these microbiome–BA interactions, contributing to the heterogeneity of dietary intervention responses. Overall, the literature supports a model in which microbiome-derived BA profiles act as metabolic phenotypes that shape host lipid and glucose homeostasis, inflammation, and gut–liver axis integrity. Emerging clinical applications include microbiome-stratified dietary strategies, targeted probiotics with defined BA-modifying functions, and therapeutic approaches that align BA-modulating interventions with an individual’s microbial metabolic capacity. Establishing integrated biomarker platforms combining microbiome clustering with BA profiling will be essential for advancing precision nutrition and personalized management of metabolic and gastrointestinal diseases. Full article
(This article belongs to the Special Issue Gut Microbiota, Metabolites, and Immune Regulation in Gastrointestinal Diseases)
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