Role of Dietary Nutrients in the Modulation of Gut Microbiota

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Gut Microbiota".

Deadline for manuscript submissions: 31 October 2025 | Viewed by 3526

Special Issue Editors


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Guest Editor
Centro de Apoio Tecnológico Agro Alimentar (CATAA), Castelo Branco, Portugal
Interests: gut microbiota; diet; immunomodulation; cardiometabolic health; gut-lung axis; dietary intervention studies

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Guest Editor
IBMC/I3S, Faculty of Medicine of Porto, Hospital S João, Porto, Portugal
Interests: microbiota; immunomodulation; Host Health

Special Issue Information

Dear Colleagues,

The interactions between diet, gut microbiota, and host health are intricate and multifaceted. Dietary patterns significantly influence the composition and function of the gut microbiota, which in turn affects host health through the production of various metabolites. These metabolites can have both beneficial and adverse effects on the host. Different components of the diet, such as protein, saturated and unsaturated fats, carbohydrates, and fibre influence the abundance of different types of bacteria in the gut, thereby regulating the gut microbiota's impact on health and disease. Emerging research highlights how gut microbiota also mediate immunomodulation and communicate with distal organs via the lymphatic and circulatory systems. This "common mucosal response" suggests that the gut microbiota and their metabolites influence not only local intestinal immunity but also immune responses in distant tissues, such as the lungs. Although the precise mechanisms remain unclear, systemic propagation of bacterial-derived components, metabolites, and migrating immune cells is implicated in this inter-organ communication. Furthermore, bidirectional interactions are evident; for instance, short-chain fatty acids from the gut can affect lung homeostasis and influence immune cell development in the bone marrow. By bridging the gap between diet and gut microbiota, this Special Issue seeks to elucidate the role of dietary nutrients in shaping gut microbiota and the broader implications for host health and disease. The exploration of mechanisms underlying local and systemic immune responses will be considered as an additional point of focus.

Dr. Inês Brandão
Dr. Joana Ferreira-Gomes
Guest Editors

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Keywords

  • gut microbiota
  • diet
  • immunomodulation
  • dietary intervention studies

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Published Papers (2 papers)

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Research

17 pages, 1103 KB  
Article
In Vitro Probiotic Modulation of Specific Dietary Complex Sugar Consumption in Fecal Cultures in Infants
by Daniela Mollova, Vesselin Baev and Ilia Iliev
Microorganisms 2025, 13(10), 2352; https://doi.org/10.3390/microorganisms13102352 - 14 Oct 2025
Viewed by 262
Abstract
Establishing the relative stability of the gastrointestinal microbiome after birth is a long and complex process, and it occurs under various influences. The human gut microbiome plays a crucial role in influencing an individual’s health and well-being across all stages of life. Breastfeeding, [...] Read more.
Establishing the relative stability of the gastrointestinal microbiome after birth is a long and complex process, and it occurs under various influences. The human gut microbiome plays a crucial role in influencing an individual’s health and well-being across all stages of life. Breastfeeding, the introduction of solid food at a certain stage after birth, and the type of food largely determine the composition of the developing microbiome. The influence of probiotics on the early development of the microbiome is gaining increasing interest. The method of in vitro co-cultivation with probiotic strains provides a clearer picture of the influence of these microorganisms on the community and the functional changes that the infant’s microbiome undergoes. We used fecal samples to study this influence by conducting metagenomic sequencing to determine the composition of the microbiome and a series of cultivations to determine the absorption of various fibers and prebiotic sugars from breast milk. We found statistically significant differences in the absorption of prebiotic sugars isolated from breast milk, as well as better absorption of several substrates in the presence of a probiotic strain. Full article
(This article belongs to the Special Issue Role of Dietary Nutrients in the Modulation of Gut Microbiota)
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15 pages, 1081 KB  
Article
Effects of Dietary Fiber Supplementation on Gut Microbiota and Bowel Function in Healthy Adults: A Randomized Controlled Trial
by Ryo Inoue, Kenta Suzuki, Masachika Takaoka, Michihiro Narumi and Yuji Naito
Microorganisms 2025, 13(9), 2068; https://doi.org/10.3390/microorganisms13092068 - 5 Sep 2025
Viewed by 2722
Abstract
This randomized, double-blind, controlled trial evaluated the effects of 4-week dietary fiber supplementation on gut microbiota, bowel-related quality of life, and secondary outcomes, including sleep and skin condition. A total of 105 healthy adults received either low-fiber foods (2.2 g/day total fiber, 1.2 [...] Read more.
This randomized, double-blind, controlled trial evaluated the effects of 4-week dietary fiber supplementation on gut microbiota, bowel-related quality of life, and secondary outcomes, including sleep and skin condition. A total of 105 healthy adults received either low-fiber foods (2.2 g/day total fiber, 1.2 g/day fermentable fiber) or high-fiber foods (8.2 g/day total fiber, including 6.4 g/day fermentable fiber). Gut microbiota was analyzed by 16S rRNA sequencing. Outcomes included stool diary, JPAC-QOL (Japanese version of the Patient Assessment of Constipation Quality of Life), OSA-MA (Oguri-Shirakawa-Azumi sleep inventory MA version), skin questionnaires, and fecal organic acids. The high-fiber group showed significant improvements in JPAC-QOL and increases in SCFA-associated genera such as Anaerostipes, Bifidobacterium, and Fusicatenibacter. These taxa positively correlated with other beneficial bacteria, including Faecalibacterium, suggesting ecological cooperation. The effects on sleep and skin were limited but correlated with beneficial bacteria, implying possible gut–brain and gut–skin axes involvement. This study demonstrated that short-term fiber supplementation meaningfully improved the bowel-related quality of life and beneficially modulated the gut microbiota in healthy adults. Although the systemic effects were modest, microbial shifts suggest that higher fiber intake may provide broader health benefits with longer interventions. This study was registered in the UMIN Clinical Trial Registry (UMIN000054712). Full article
(This article belongs to the Special Issue Role of Dietary Nutrients in the Modulation of Gut Microbiota)
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