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Microbiome-Immunity Crosstalk and Its Role in Health and Disease

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (20 February 2026) | Viewed by 6399

Special Issue Editors


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Guest Editor

E-Mail Website
Guest Editor
NBC Group, Psychology Department, School of Life and Nature Sciences, Nebrija University, 28248 Madrid, Spain
Interests: cognition; memory; microbiota; neurodegenerative diseases

Special Issue Information

Dear Colleagues,

The human body is home to an extensive and diverse array of microorganisms, collectively termed the microbiome. These microbial communities, particularly those in the gut, engage in continuous interaction with the immune system, shaping its development, functionality, and stability. This bidirectional communication, known as microbiome–immunity interaction, plays a pivotal role in preserving health and preventing illness. Both the innate and adaptive immune systems are profoundly shaped by microbial exposure. The colonization of the body by beneficial microbes during early life is essential for immune system maturation, guiding immune cell differentiation and response mechanisms. Disruptions in this delicate equilibrium, often due to external influences such as diet, antibiotics, or infections, can lead to immune system imbalances, increasing vulnerability to various conditions. Despite remarkable progress in microbiome research, challenges persist in proving causal links between microbiota alterations and disease. A comprehensive understanding of host–microbiota interactions will require integrating multi-omics approaches, including metagenomics, metabolomics, and immunoprofiling. Furthermore, the development of microbiome-targeted treatments, such as probiotics, prebiotics, and fecal microbiota transplants, offers promising avenues for managing immune-related conditions. Therefore, the aim of this Research Topic is to study the microbiome–immunity interaction. Given its crucial role in human health by shaping immune functions and influencing disease susceptibility, this research seeks to gain deeper insight into these interactions and explore innovative therapeutic approaches to modify the microbiome in support of immune balance and disease prevention. The following topics are proposed for the SI:

  • Microorganisms involved in the maturation and modulation of the immune system;
  • The immune system’s modulation of the microbiome;
  • Microbiota, immune system, and brain: impacts on neurodegenerative diseases;
  • Inflammatory processes associated with dysbiosis;
  • The role of commensal host microbiota in regulating microglial development and homeostasis;
  • Dysbiosis and autoimmune, inflammatory, and metabolic diseases;
  • Prebiotics, probiotics, and psychobiotics in immune-mediated disorders;
  • Lifestyle habits such as diet, exercise, environment, and/or use of antibiotics and drugs;
  • Clinical applications of the use of new interventions in chronic pathologies.

Prof. Dr. Ana Isabel Beltrán-Velasco
Dr. Sara Uceda
Guest Editors

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Keywords

  • gut microbiota
  • immune system
  • nutrition
  • inflammatory processes
  • dysbiosis
  • neurodegenerative diseases

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Published Papers (5 papers)

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Research

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18 pages, 1320 KB  
Article
AI-Guided Multi-Omic Microbiome Modulation Improves Clinical and Inflammatory Outcomes in Refractory IBD: A Real-World Study
by Raluca Lupusoru, Lavinia Cristina Moleriu, Ruxandra Mare, Ioan Sporea, Alina Popescu, Roxana Sirli, Adrian Goldis, Camelia Nica, Tudor Voicu Moga, Bogdan Miutescu, Iulia Ratiu, Oana Belei, Laura Olariu, Victor Dumitrascu and Radu Dumitru Dragomir
Int. J. Mol. Sci. 2026, 27(1), 201; https://doi.org/10.3390/ijms27010201 - 24 Dec 2025
Viewed by 2177
Abstract
Inflammatory bowel disease (IBD) remains difficult to manage in patients who fail multiple therapeutic lines, and growing evidence suggests that alterations in the gut microbiome contribute to persistent symptoms and inflammatory activity. This study evaluated a three-month, AI-guided, multi-omic personalized microbiome modulation program [...] Read more.
Inflammatory bowel disease (IBD) remains difficult to manage in patients who fail multiple therapeutic lines, and growing evidence suggests that alterations in the gut microbiome contribute to persistent symptoms and inflammatory activity. This study evaluated a three-month, AI-guided, multi-omic personalized microbiome modulation program in adults with treatment-refractory IBD. Baseline stool metagenomic sequencing, blood biomarkers, micronutrient panels, and clinical data were integrated through an artificial intelligence platform to generate individualized plans combining dietary adjustments, targeted synbiotics, selective antimicrobials, and micronutrient correction. Clinical outcomes, inflammatory markers, and microbial signatures were reassessed after three months. Across 358 participants, stool frequency decreased substantially, urgency and rectal bleeding resolved in most patients, and over 70% reported a “much improved” overall condition. Inflammatory biomarkers showed marked normalization, with reductions in hs-CRP and fecal calprotectin observed in over 85% of cases. Micronutrient deficiencies, particularly iron and zinc, also improved, and beneficial microbial taxa such as Faecalibacterium prausnitzii, Bifidobacterium longum, and Akkermansia muciniphila increased significantly. These findings suggest that personalized, multi-omic microbiome modulation may support clinically meaningful improvements by targeting microbial, metabolic, and immune imbalances rather than symptoms alone. While encouraging, these results require confirmation in randomized controlled studies. Full article
(This article belongs to the Special Issue Microbiome-Immunity Crosstalk and Its Role in Health and Disease)
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17 pages, 8989 KB  
Article
Cysteine Attenuates Intestinal Inflammation by Regulating the Gut Microbiota and TLR4-JNK/MAPK-NF-κB Pathway in Piglets
by Rui Liu, Pengxiang Qin, Zihao Liu, Wenjing Liu, Shuzhen Jiang, Xuejun Yuan, Weiren Yang, Caiyun Huang and Ning Jiao
Int. J. Mol. Sci. 2025, 26(24), 11991; https://doi.org/10.3390/ijms262411991 - 12 Dec 2025
Viewed by 569
Abstract
As a nutritionally important amino acid, cysteine (Cys) could attenuate oxidative damage on growth performance and intestinal barrier function in piglets. However, the mechanism of Cys in attenuating intestinal injury remains unclear. The aim of this study was to investigate the mechanism of [...] Read more.
As a nutritionally important amino acid, cysteine (Cys) could attenuate oxidative damage on growth performance and intestinal barrier function in piglets. However, the mechanism of Cys in attenuating intestinal injury remains unclear. The aim of this study was to investigate the mechanism of Cys in defending against intestinal inflammation in piglets. A total of twenty-four piglets were divided into four groups and fed a diet with or without 0.1% BPA or Cys for a 28 d feeding trial. The results showed that Cys supplementation reinstated the jejunal barrier by increasing cell proliferation and the goblet cell number, and decreased cell apoptosis upon BPA exposure. Cys supplementation also decreased serum and jejunal pro-inflammatory cytokine and immunoglobulin levels in BPA-challenged piglets. Furthermore, Cys mitigated inflammation by normalizing the activation of the toll-like receptor 4 (TLR4)-JNK/MAPK-nuclear factor-kappa B (NF-κB) pathway caused by BPA. Additionally, dietary Cys supplementation restored the levels of butyrate, valerate and isovalerate in cecum contents that were decreased by BPA exposure. Meanwhile, Cys supplementation normalized the abundances of Prevotellaceae and Romboutsia upon BPA exposure. In conclusion, Cys is critical to nutrition through attenuating intestinal inflammation by regulating gut microbial balance and suppressing the TLR4-JNK/MAPK-NF-κB pathway. Full article
(This article belongs to the Special Issue Microbiome-Immunity Crosstalk and Its Role in Health and Disease)
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Review

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28 pages, 2858 KB  
Review
Enteric Infections, Dysbiosis, and Metabolic Dysfunction: The Role of Diarrheagenic Pathogens in Insulin Resistance
by Martin Zermeño-Ruiz, Filiberto Gutierrez-Gutierrez, Elsa Janneth Anaya-Ambriz, Emiliano Peña-Durán, Jesús Jonathan García-Galindo, Alfredo Huerta-Huerta, Araceli Lizbeth Quiñonez-Gallardo and Daniel Osmar Suárez-Rico
Int. J. Mol. Sci. 2026, 27(3), 1610; https://doi.org/10.3390/ijms27031610 - 6 Feb 2026
Viewed by 398
Abstract
Type 2 diabetes and insulin resistance are increasingly recognized as conditions influenced not only by genetic and lifestyle factors but also by infectious and microbial exposures. Diarrheagenic pathogens, including enterotoxigenic, enteroaggregative, and enterohemorrhagic Escherichia coli, as well as other enteric microorganisms, disrupt [...] Read more.
Type 2 diabetes and insulin resistance are increasingly recognized as conditions influenced not only by genetic and lifestyle factors but also by infectious and microbial exposures. Diarrheagenic pathogens, including enterotoxigenic, enteroaggregative, and enterohemorrhagic Escherichia coli, as well as other enteric microorganisms, disrupt the gut microbiota and compromise intestinal barrier integrity. These alterations promote dysbiosis, increased intestinal permeability, and systemic exposure to lipopolysaccharides and other microbial products, leading to metabolic endotoxemia and chronic low-grade inflammation. In parallel, pathogen-induced modulation of host immune responses contributes to adipose tissue inflammation, mitochondrial dysfunction, and impaired insulin signaling. This review summarizes current evidence linking diarrheagenic pathogens to insulin resistance, with emphasis on the microbiota–immune–metabolism axis. Understanding these interactions highlights novel perspectives on the pathogenesis of insulin resistance and suggests that targeted modulation of the gut microbiota or reduction in pathogen-driven inflammation may represent therapeutic opportunities to improve metabolic outcomes. Full article
(This article belongs to the Special Issue Microbiome-Immunity Crosstalk and Its Role in Health and Disease)
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17 pages, 592 KB  
Review
Butyrate-Producing Bacteria as a Keystone Species of the Gut Microbiome: A Systemic Review of Dietary Impact on Gut–Brain and Host Health
by Jacob L. Snodgrass and Bisi T. Velayudhan
Int. J. Mol. Sci. 2026, 27(3), 1289; https://doi.org/10.3390/ijms27031289 - 28 Jan 2026
Viewed by 1021
Abstract
The human gut microbiome is a complex ecosystem integral to host health, with butyrate-producing bacteria (BPB) playing a critical role in maintaining intestinal homeostasis. This scoping review explores the composition, function, and systemic influence of BPB, focusing on their metabolic product, butyrate, and [...] Read more.
The human gut microbiome is a complex ecosystem integral to host health, with butyrate-producing bacteria (BPB) playing a critical role in maintaining intestinal homeostasis. This scoping review explores the composition, function, and systemic influence of BPB, focusing on their metabolic product, butyrate, and its implications for gut integrity, immune modulation, and gut–brain axis (GBA) communication. Disruptions to BPB abundance, which is correlated with Western dietary patterns, food additives, and antibiotic exposure, are linked to gut dysbiosis and associated with a wide spectrum of chronic diseases, including inflammatory bowel disease (IBD), obesity, type 2 diabetes, neurodegenerative disorders, and psychiatric conditions. Butyrate supports colonocyte energy metabolism, reinforces epithelial barrier function, regulates goblet cell mucus production, and exerts anti-inflammatory effects via histone deacetylase inhibition and G-protein-coupled receptor signaling. The depletion of BPB and the resultant butyrate deficiency may represent a unifying pathophysiological mechanism underlying these conditions. Therapeutic strategies that restore BPB populations and butyrate levels, such as prebiotics, dietary fiber, and microbiota-targeted interventions, hold promise for mitigating inflammation and enhancing systemic health through microbiome modulation. Full article
(This article belongs to the Special Issue Microbiome-Immunity Crosstalk and Its Role in Health and Disease)
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20 pages, 1809 KB  
Review
Exploring the Diagnostic and Predictive Value of Oral Microbiome in Esophageal Cancer: A Systematic Review and Meta-Analysis
by Jie-Chi Chen, Min-Hsun Hsu, Suh-Woan Hu and Yuh-Yih Lin
Int. J. Mol. Sci. 2025, 26(19), 9457; https://doi.org/10.3390/ijms26199457 - 27 Sep 2025
Cited by 1 | Viewed by 1661
Abstract
The research interest in the oral microbiome’s role in esophageal cancer is growing, yet a comprehensive synthesis of available evidence is still lacking. This study aimed to explore the effects of oral microbiome on the development of esophageal cancer through a systematic review [...] Read more.
The research interest in the oral microbiome’s role in esophageal cancer is growing, yet a comprehensive synthesis of available evidence is still lacking. This study aimed to explore the effects of oral microbiome on the development of esophageal cancer through a systematic review of existing literature retrieved from the Embase, PubMed, and Web of Science databases. Eighteen studies published between 2015 and 2024 were obtained, involving 1191 cases and 1403 controls, mostly using oral saliva samples and 16S rRNA gene sequencing. Findings on alpha-diversity were inconsistent, while most studies reported significant beta-diversity differences between cases and controls. Notably, several investigations on esophageal squamous cell carcinoma showed higher levels of Prevotella, Porphyromonas, and Fusobacterium, while two studies on esophageal adenocarcinoma reported elevated levels of Actinomyces species. A fixed-effect meta-analysis of two studies showed that individuals with specific oral microbial signatures had significantly higher odds of developing esophageal squamous cell carcinoma (OR = 9.50; 95% CI: 5.89–15.29). Quality assessments highlighted methodological strengths but noted variability in group comparability and local applicability. These results reveal the potential of oral microbiome shift as an early detection biomarker and for developing personalized strategies in treating esophageal cancer, meriting further clinical investigation. Full article
(This article belongs to the Special Issue Microbiome-Immunity Crosstalk and Its Role in Health and Disease)
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