cimb-logo

Journal Browser

Journal Browser

Molecular Mechanisms of Gut Microbiota in Health, Immunity and Disease

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (31 October 2025) | Viewed by 11938

Special Issue Editor


E-Mail Website
Guest Editor
Plants for Human Health Institute, Department of Food Bioprocessing and Nutrition Sciences, North Carolina State University, 600 Laureate Way, Kannapolis, NC 28081, USA
Interests: probiotics; bifidobacterium; bactobacillus; gut microbiome; CVD; diabetes; colitis; atherosclerosis; miRNA; drugs; antibiotic resistance; nutrients; metabolism; metabolites
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The complexity of the gut microbiome, which has far-reaching effects on all aspects of health, has made it a vital topic in research, enhancing our understanding of human physiology and pathology. Trillions of microorganisms, including bacteria, viruses, fungi, and archaea, make up the gut microbiome and communicate with the host using complex molecular mechanisms that affect multiple biological systems. Such interactions not only sustain digestive health but also modulate immune responses, affect metabolism, and interact with the central nervous system through the gut–brain axis. In this context, this Special Issue aims to explore this complex interplay further by deciphering the molecular crosstalk between gut microorganisms and the host. We aim to offer detailed insights into how the microbiota contribute to homeostasis, what goes wrong with dysbiosis, and how these changes correlate with either health benefits or disease states. By spotlighting the most recent advances in microbiota research, this Special Issue aims to expose the molecular bases by which microbiota are influencing immunity, inflammation, and chronic conditions, providing unprecedented insights into potential diagnostic and therapeutic strategies. Studies focused on broader areas of dietary-based therapeutic interventions, including prebiotics, probiotics, and targeting the microbiome, will be considered as well.

The human gut microbiota is a critical determinant of health and disease, functioning as a dynamic ecosystem that interacts intricately with its host. This Special Issue aims to provide a platform for cutting-edge research that explores the molecular mechanisms through which gut microbiota influence health, contribute to disease processes, and modulate immune responses. The scope of this Special Issue encompasses, but is not limited to, the following areas: gut microbiota and host health, microbiota in disease pathogenesis, immune system modulation by microbiota, microbiota-driven therapeutics, multi-omics and advanced methodologies, and environmental and lifestyle influences.

We invite submissions focusing on, but not limited to, the following topics:

  • Gut microbiota and host health;
  • Microbiota in disease pathogenesis;
  • Immune system modulation by microbiota;
  • Microbiota-driven therapeutic strategies;
  • Multi-omics and advanced methodologies in microbiome research;
  • Environmental and lifestyle influences on the microbiome.

By addressing these topics, this Special Issue aims to provide a comprehensive platform for cutting-edge research and foster advancements in our understanding of the gut microbiome’s molecular mechanisms.

Dr. Ahmad Ud Din
Guest Editor

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. Current Issues in Molecular Biology is an international peer-reviewed open access monthly 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 2200 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 microbiome
  • immune system
  • probiotics
  • prebiotics
  • microbial metabolites
  • microbiota–host interactions
  • gut–brain axis

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

13 pages, 604 KB  
Article
Preliminary Study on Circulating REG3α and Its Associations with Vitamin D Supplementation and Inflammatory Biomarkers in Adults with Overweight and Obesity
by Theocharis Koufakis, Dimitrios Kouroupis, Areti Kourti, Paraskevi Karalazou, Katerina Thisiadou, Ioannis Georgiadis, Omar Mustafa, Giuseppe Maltese, Luca Busetto, Djordje S. Popovic, Olga Giouleme, Kalliopi Kotsa, Michael Doumas and Kali Makedou
Curr. Issues Mol. Biol. 2025, 47(12), 970; https://doi.org/10.3390/cimb47120970 - 21 Nov 2025
Viewed by 497
Abstract
Objective: Obesity is characterized by chronic inflammation and gut dysbiosis, yet circulating markers reflecting intestinal immune activation remain limited. Regenerating islet-derived protein 3 alpha (REG3α), an antimicrobial peptide secreted by intestinal Paneth cells, plays a pivotal role in mucosal defense and mirrors microbial–epithelial [...] Read more.
Objective: Obesity is characterized by chronic inflammation and gut dysbiosis, yet circulating markers reflecting intestinal immune activation remain limited. Regenerating islet-derived protein 3 alpha (REG3α), an antimicrobial peptide secreted by intestinal Paneth cells, plays a pivotal role in mucosal defense and mirrors microbial–epithelial interactions. In this cross-sectional study, we aimed to examine circulating REG3α levels in infection-free adults with obesity, overweight, and normal weight, and to explore their associations with vitamin D supplementation and biomarkers of inflammation and dysbiosis. Methods: Sixty-nine participants were stratified into control, overweight, and obesity groups. Serum REG3α, interleukin-6 (IL-6), β-defensin-2, high-sensitivity c-reactive protein, ferritin, and presepsin were assessed. Vitamin D status and supplementation history were recorded. Multivariable linear regression, principal component analysis (PCA), and bootstrap mediation models were applied to explore associations and potential indirect effects. Results: REG3α concentrations were higher in overweight and obesity compared to controls (646 ± 217 vs. 521 ± 311 ng/mL); however, the difference was not significant (p = 0.15). Vitamin D supplementation was inversely associated with REG3α (p = 0.06), and this effect appeared weaker in obesity. REG3α correlated positively with IL-6 (ρ = 0.28) and β-defensin-2 (ρ = 0.43). PCA revealed a shared inflammatory–mucosal activation component that predicted REG3α levels. Exploratory mediation suggested a partial indirect effect of vitamin D via reduced inflammatory activity. Conclusions: Circulating REG3α shows associations with indicators of inflammation and vitamin D supplementation in individuals with overweight and obesity. Although differences between groups did not reach statistical significance, the observed trends suggest possible links between mucosal immune activity and metabolic status. These exploratory results warrant validation in larger, longitudinal studies before any biomarker role can be established. Full article
Show Figures

Figure 1

Review

Jump to: Research

42 pages, 1227 KB  
Review
Microbial Metabolomes in Alzheimer’s Disease: From Pathogenesis to Therapeutic Potential
by Alejandro Borrego-Ruiz and Juan J. Borrego
Curr. Issues Mol. Biol. 2025, 47(9), 724; https://doi.org/10.3390/cimb47090724 - 5 Sep 2025
Cited by 1 | Viewed by 2347
Abstract
Background: Accumulating evidence underscores the potential role of the gut microbiome in the pathogenesis of Alzheimer’s disease, but much remains to be clarified. This review examines current evidence linking gut microbiome dysbiosis to Alzheimer’s disease, focusing on microbial metabolomes and their mechanistic role, [...] Read more.
Background: Accumulating evidence underscores the potential role of the gut microbiome in the pathogenesis of Alzheimer’s disease, but much remains to be clarified. This review examines current evidence linking gut microbiome dysbiosis to Alzheimer’s disease, focusing on microbial metabolomes and their mechanistic role, as well as on the potential of therapeutic approaches targeting the gut microbiome. Methods: A narrative, non-systematic examination of the literature was conducted to provide a comprehensive overview of the subject under examination. Database searches were performed in PubMed, Scopus, and Web of Science between June and July 2025. Results: Alzheimer’s disease is linked to reduced gut microbial diversity and altered bacterial taxa. Gut microbiome shifts correlate with inflammation and may drive Alzheimer’s disease progression via the microbiota–gut–brain axis. Microbial amyloids and bacterial products can cross both the intestinal and blood–brain barrier, triggering neuroinflammation and promoting amyloid and tau pathologies. Short-chain fatty acids produced by the gut microbiome regulate neuroinflammation, lipid metabolism, and gene expression, impacting Alzheimer’s disease pathology. Therapeutics targeting the gut microbiome, including probiotics, prebiotics, and fecal microbiota transplantation, show promise in modulating neuroinflammation, reducing amyloid and tau pathology, and improving cognitive function in Alzheimer’s disease. Conclusions: The gut microbiome significantly influences Alzheimer’s disease pathogenesis, and its modulation offers potential to slow progression. However, further research is required to validate effective clinical interventions. Full article
Show Figures

Figure 1

36 pages, 1957 KB  
Review
Rewiring the Brain Through the Gut: Insights into Microbiota–Nervous System Interactions
by Ilinca Savulescu-Fiedler, Serban-Nicolae Benea, Constantin Căruntu, Andreea-Simona Nancoff, Corina Homentcovschi and Sandica Bucurica
Curr. Issues Mol. Biol. 2025, 47(7), 489; https://doi.org/10.3390/cimb47070489 - 26 Jun 2025
Cited by 6 | Viewed by 8481
Abstract
The gut-brain axis (GBA) represents an operant acting in a two-direction communication system between the gastrointestinal tract and the central nervous system, mediated by the enteric nervous system (ENS), vagus nerve, immune pathways, and endocrine signaling. In recent years, evidence has highlighted the [...] Read more.
The gut-brain axis (GBA) represents an operant acting in a two-direction communication system between the gastrointestinal tract and the central nervous system, mediated by the enteric nervous system (ENS), vagus nerve, immune pathways, and endocrine signaling. In recent years, evidence has highlighted the pivotal role of the gut microbiota in modulating this axis, forming the microbiota-gut-brain axis (MGBA). Our review synthesizes current knowledge on the anatomical and functional substrates of gut-brain communication, focusing on interoceptive signaling, the roles of intrinsic primary afferent neurons (IPANs) and enteroendocrine cells (EECs) and the influence of microbial metabolites, including short-chain fatty acids (SCFAs), bile acids, and indoles. These agents modulate neurotransmission, epithelial barrier function, and neuroimmune interactions. The vagus nerve serves as a primary pathway for afferent sensory signaling from the gut influenced indirectly by the ENS and microbiota. Dysbiosis has been associated with altered gut-brain signaling and implicated in the pathophysiology of disorders ranging from irritable bowel syndrome to mood disorders and neurodegeneration. Microbial modulation of host gene expression via epigenetic mechanisms, including microRNAs, adds another layer of complexity. The gut has a crucial role as an active sensory and signaling organ capable of influencing higher-order brain functions. Understanding the MGBA has significant implications for new therapeutic interventions targeting the microbiome to manage neurogastroenterological and even neuropsychiatric conditions. Full article
Show Figures

Figure 1

Back to TopTop