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Modulation of the Intestinal Microbiome in Chronic Diseases: Mechanisms, Nutritional Interventions, and Clinical Implications

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Dr. Maria Adriana Neag

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Department of Pharmacology, Toxicology and Clinical Pharmacology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
Interests: intestinal microbiome; gut dysbiosis; chronic diseases; probiotics; prebiotics; postbiotics; microbiota modulation; host–microbiome interactions; metabolic disorders

Special Issue Information

Dear Colleagues,

The intestinal microbiome plays a fundamental role in regulating host metabolism, immune function, and overall health. In recent years, a growing body of evidence has demonstrated that disruptions in gut microbial balance—commonly referred to as dysbiosis—are closely associated with the development and progression of numerous chronic diseases, including metabolic disorders, gastrointestinal conditions, cardiovascular diseases, and neurological pathologies. Consequently, strategies aimed at modulating the intestinal microbiome have attracted increasing attention as promising approaches for disease prevention and therapeutic intervention.

This Special Issue seeks to explore recent advances in understanding the mechanisms linking gut microbiota to the pathophysiology of chronic diseases, while also highlighting innovative approaches for microbiome modulation. Particular emphasis will be placed on the potential roles of prebiotics, probiotics, postbiotics, dietary interventions, and microbiota-targeted nutritional therapies in restoring microbial balance and promoting host health. Submissions focusing on molecular pathways, host–microbiome interactions, translational research, and clinical evidence are especially encouraged.

By bringing together original research articles and comprehensive review papers, this Special Issue aims to provide an updated overview of microbiome-centered strategies and their potential contribution to the prevention and management of chronic diseases.

Dr. Maria Adriana Neag
Guest Editor

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Review

21 pages, 4248 KB

Open AccessReview

Beyond Bacteria: The Emerging Role of the Gut Virome and Mycobiome in Celiac Disease

by Aurelio Seidita, Mirco Pistone, Federica Latteri, Francesca Di Stefano, Pasquale Mansueto, Sonia Giardina, Gabriele Spagnuolo, Alessandro Termini, Salvatore Maestri, Alessandra Giuliano, Salvatore Accomando, Carola Buscemi, Francesca Mandreucci and Antonio Carroccio

Nutrients 2026, 18(16), 2721; https://doi.org/10.3390/nu18162721 - 20 Aug 2026

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Abstract

Background/Objectives: Celiac disease (CeD) is a complex autoimmune enteropathy triggered by gluten intake in genetically predisposed individuals. While the bacterial microbiome has been extensively studied in CeD, the role of the gut virome and mycobiome is less well defined. Emerging evidence suggests that viruses and fungi may influence mucosal immunity, intestinal permeability and gluten tolerance, acting as potential environmental cofactors in the onset of this disease. Methods: A narrative review of the literature was conducted to summarize current knowledge of the composition, development and function of the gut virome and mycobiome and to explore their potential involvement in CeD pathogenesis. Results: The gut virome shows high interindividual variability and dynamic maturation early in life. Multiple studies have associated early enterovirus or parechovirus infections with an increased risk of celiac autoimmunity, supporting a virus–gluten “double hit” model. Viral dysbiosis in CeD has been reported to include an enrichment of human polyomavirus 2 (JC polyomavirus) and of specific enterobacterial phages. The mycobiome, although less abundant, also displays disease-associated alterations: cross-sectional mycobiome studies have reported higher relative abundance of Saccharomyces, Candida, and Tricholomataceae and lower relative abundance of Pichia and Pneumocystis taxa in children with CeD. Conclusions: Current evidence, although preliminary, supports associations between selected viral exposures and CeD-related immune alterations, whereas current phageome and mycobiome findings mainly describe cross-sectional compositional differences. These data do not establish temporal direction or causality, and further longitudinal and mechanistic investigations are required before preventive or therapeutic implications can be considered. Full article

(This article belongs to the Special Issue Modulation of the Intestinal Microbiome in Chronic Diseases: Mechanisms, Nutritional Interventions, and Clinical Implications)

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19 pages, 1223 KB

Open AccessReview

Whole and Sprouted Cereals as Nutritional Modulators of the Gut Microbiota and Intestinal Inflammation in IBD

by Valentina Álvarez-Arraño, Karen Toledo-Stuardo, Marjo J. E. Campmans-Kuijpers, Fabien Magne and Marcela A. Hermoso

Nutrients 2026, 18(15), 2447; https://doi.org/10.3390/nu18152447 - 27 Jul 2026

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Abstract

Ulcerative colitis (UC) and Crohn’s disease (CD), known as inflammatory bowel diseases (IBDs), result from a complex interaction of genetic, immunological, microbial and environmental factors. There is growing evidence suggesting that imbalances in the gut microbiota, or dysbiosis, play a causal role in IBD and are strongly influenced by aspects of the Western lifestyle. Diet is an important modulator of gut health, and whole cereals have attracted attention for their potential to positively shape gut microbiota and intestinal function. Germination further enhances the content of prebiotic substrates and bioactive compounds such as polyphenols, GABA and fiber, which may modulate inflammation, oxidative stress and immune responses. In vitro and clinical studies suggest that these compounds may reduce pro-inflammatory cytokines and improve symptoms in IBD, although robust evidence in patients is still lacking. Here, we provide an overview of whole and sprouted cereals and their effects on inflammation and gut microbiota, with particular focus on IBD. We also discuss the potential of sprouted grains as a complementary approach to diet alongside conventional therapy, highlighting their possible support to gut health to mitigate inflammation. Finally, we emphasize the need for further well-designed clinical studies to confirm their therapeutic potential and to better understand the mechanisms underlying their beneficial effects. Full article

(This article belongs to the Special Issue Modulation of the Intestinal Microbiome in Chronic Diseases: Mechanisms, Nutritional Interventions, and Clinical Implications)

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