Interactions Between Gut Microbiota and Epigenetic Markers in Health and Disease

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell and Gene Therapy".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 1244

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Guest Editor
Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
Interests: gut microbiome; epigenetic marks; metabolic diseases; neuropsychiatric disorders; inflammatory diseases
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Special Issue Information

Dear Colleagues,

Environmental factors such as microbes, diet, and pharmaceuticals significantly influence the development and progression of various diseases, including cancers, neuropsychiatric, cardiovascular, metabolic, autoimmune, and inflammatory disorders. These complex conditions result from dynamic interactions among the gut microbiota, their metabolites, host genetics, epigenetic regulation, and immune responses. Epigenetic modifications—such as DNA methylation, histone modification, and non-coding RNA regulation—govern key cellular processes like proliferation, apoptosis, inflammation, and immune function, thereby shaping disease onset and progression. Recent evidence highlights that microbiota-derived metabolites, particularly short-chain fatty acids, can modulate epigenetic mechanisms by inhibiting histone deacetylases and altering DNA methylation, ultimately influencing gene expression and critical physiological processes such as immune regulation, mucosal integrity, metabolism, and organ function. This Special Issue of Cells focuses on recent advances in elucidating the interplay between intestinal microbiota and epigenetic regulation in disease pathogenesis and therapy. It welcomes studies exploring how diet and environmental exposures affect health outcomes through epigenetic modulation, as well as mechanistic insights into microbiota–host gene regulation across diverse diseases (cancers, neuropsychiatric disorders, cardiovascular diseases, metabolic diseases, infectious diseases, autoimmune, gastrointestinal, and inflammatory diseases, and opioid addiction). By integrating multidisciplinary research, this Special Issue aims to advance understanding of microbiota–epigenome interactions and foster the development of novel, microbiota-targeted epigenetic therapies for precision medicine.

Dr. Shabnam Nohesara
Guest Editor

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Keywords

  • gut microbiome
  • epigenetic marks
  • cancer
  • metabolic diseases
  • neuropsychiatric disorders
  • inflammatory diseases
  • infectious diseases
  • cardiovascular diseases
  • probiotics
  • prebiotics

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Published Papers (1 paper)

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Review

28 pages, 1591 KB  
Review
Epigenetic Modulators: Role of Gut Microbiome in Transformation of Nutrient Bioactives and Host Gene Regulation
by Hadeel Edkaidek, Divakar Dahiya and Poonam Singh Nigam
Cells 2026, 15(11), 957; https://doi.org/10.3390/cells15110957 - 22 May 2026
Viewed by 847
Abstract
Biological activity of diets consisting of dietary fibers, peptides and polyphenols is largely mediated by the gut microbiota, which converts these compounds into bioactive metabolites. This review examines the microbiota–epigenome axis, highlighting gut microbiota-derived metabolites, including short-chain fatty acids (SCFAs), urolithins, and phenolic [...] Read more.
Biological activity of diets consisting of dietary fibers, peptides and polyphenols is largely mediated by the gut microbiota, which converts these compounds into bioactive metabolites. This review examines the microbiota–epigenome axis, highlighting gut microbiota-derived metabolites, including short-chain fatty acids (SCFAs), urolithins, and phenolic acids, that modulate host gene expression through DNA methylation, histone modifications, and non-coding RNA regulation. Current evidence from molecular and microbiome studies indicates that these metabolites influence key metabolic and inflammatory pathways, including lipid absorption via CD36, SIRT1 activation, and one-carbon metabolism involving folate and S-adenosylmethionine (SAM). Inter-individual variability in metabolic responses is associated with differences in microbial composition and metabotypes, which determine the magnitude of epigenetic regulation. Furthermore, dietary polyphenols derived from pomegranate, berries, tea, cocoa, and grapes are shown to modulate gut microbiota composition and enhance epigenetic effects. A “butyrate–polyphenol synergy” model is proposed, in which combined microbial metabolites optimize host epigenetic programming. Overall, agri-food by-products are suggested to function as modulators of the host epigenetic landscape, providing a framework for microbiome-targeted dietary strategies to improve metabolic and inflammatory health. Full article
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