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The Gut Microbiota—Its Role and Molecular Mechanisms in Nutritional Health
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The Gut Microbiota—Its Role and Molecular Mechanisms in Nutritional Health

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: 20 June 2026 | Viewed by 3357

Special Issue Editors

Prof. Dr. Xi Ma

E-Mail Website
Guest Editor
State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Interests: nutrition; gut microbiota; mucosal immunity
Special Issues, Collections and Topics in MDPI journals
Dr. Peng Tan

E-Mail Website
Guest Editor
State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Interests: animal; nutrition; microbiome

Special Issue Information

Dear Colleagues,

The healthy homeostasis of the gut microbiota has a comprehensive impact on host health, demonstrating striking similarities in both humans and animals. It profoundly affects host physiological function, disease susceptibility, and productive performance through complex metabolic networks and immunomodulatory mechanisms. Imbalance of flora is closely associated with a variety of diseases, including digestive diseases (e.g., inflammatory bowel disease, diarrhea in weaned piglets, etc.), metabolic disorders (e.g., obesity, diabetes, etc.), and immune-related (e.g., allergies, autoimmune diseases, etc.); optimizing the intestinal flora in animal production and breeding can also significantly improve feed utilization, promote growth, reduce antibiotic dependence, and simultaneously improve meat quality and food safety. We aim to explore the importance of the role and composition of the gut microbiota in maintaining host health while also emphasizing the link between dysbiosis and disease and gain a deeper understanding of the molecular principles underlying the basic physiological processes, mechanisms, biological functions, and interactions between gut microbiota, interspecies crosstalk, and the host response.

As part of this Special Issue, we aim to collect the latest insights into microbial communities, including their interactions with health and disease, ecological composition, and the immune system. We welcome papers on the molecular characteristics of microbiota regulation/remodeling, symbionts, and pathogens, in addition to their metabolomics and/or nutritional metabolic regulatory mechanisms, with a particular focus on gut microbial communities. 

Prof. Dr. Xi Ma
Dr. Peng Tan
Guest Editors

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • gut microbiota
  • microbiome
  • mucosal immunity
  • probiotics
  • omics
  • dysbiosis
  • microbiota–host interactions
  • microbiota manipulation

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Published Papers (2 papers)

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Research

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25 pages, 5688 KB  
Article
Lacticaseibacillus rhamnosus MS27 Potentially Prevents Ulcerative Colitis Through Modulation of Gut Microbiota
by Jie Zhang, Jiakun Shen, Linbao Ji, Peng Tan, Chunchen Liu, Xiujun Zhang and Xi Ma
Int. J. Mol. Sci. 2025, 26(23), 11397; https://doi.org/10.3390/ijms262311397 - 25 Nov 2025
Viewed by 1096
Abstract
(1) This study explored Lacticaseibacillus rhamnosus MS27, a newly isolated strain, as a potential probiotic candidate for alleviating the onset and severity of ulcerative colitis (UC). (2) L. rhamnosus MS27 was isolated and subjected to biochemical identification, antibiotic sensitivity testing, and antibacterial activity [...] Read more.
(1) This study explored Lacticaseibacillus rhamnosus MS27, a newly isolated strain, as a potential probiotic candidate for alleviating the onset and severity of ulcerative colitis (UC). (2) L. rhamnosus MS27 was isolated and subjected to biochemical identification, antibiotic sensitivity testing, and antibacterial activity assessment. Dextran sulfate sodium (DSS) colitis model mice were used to evaluate its alleviating effects. In this study, 16S rRNA microbiome and eukaryotes reference transcriptome analyses were conducted to investigate its impact on intestinal microbial ecology and potential molecular mechanisms. (3) L. rhamnosus MS27 exhibits high acid tolerance at pH 3.23 and maintains a high viable bacterial count for 24 h. It can utilize sucrose, lactose, maltose, inulin, esculin, salicin, and mannitol but not raffinose, and it is sensitive to carbenicillin, erythromycin, tetracycline, chloramphenicol, clindamycin, and penicillin. It effectively increases the abundance of beneficial microbes, particularly Akkermansia, Muribaculaceae, and Limosilactobacillus reuteri (p < 0.05), while significantly reducing microorganisms linked to human pathogens causing diarrhea and gastroenteritis (p < 0.05). Transcriptomic analysis demonstrated that the expression levels of Igkv16-104 and C1qtnf3 were significantly downregulated in the presence of L. rhamnosus MS27 treatment compared to DSS treatment alone (p < 0.05). Further analysis revealed significant differences in genes related to immune functions, antigen presentation, and immune cell markers, indicating potential protein–protein interaction networks, particularly among genes of the major histocompatibility complex (MHC). (4) L. rhamnosus MS27, as a novel strain, demonstrates a significant capacity to alleviate inflammatory phenotypes. L. rhamnosus MS27 exhibits distinctive metabolic characteristics in lactic acid utilization, acetic acid and oleic acid production. Furthermore, it contributes to systemic homeostasis regulation by modulating Turicibacter to link intestinal microbiota composition with host immune function. Full article
(This article belongs to the Special Issue The Gut Microbiota—Its Role and Molecular Mechanisms in Nutritional Health)
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Review

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25 pages, 2126 KB  
Review
The Role of Probiotics Limosilactobacillus reuteri, Ligilactobacillus salivarius, and Lactobacillus johnsonii in Inhibziting Pathogens, Maintaining Gut Health, and Improving Disease Outcomes
by Li Li, Xiangqi Qiu, Shengyong Lu, Haitao Yu, Panpan Lu, Sumei Zeng, Aihua Deng, Min Zhu, E Xu and Jin Niu
Int. J. Mol. Sci. 2026, 27(3), 1545; https://doi.org/10.3390/ijms27031545 - 4 Feb 2026
Viewed by 1828
Abstract
As the critical component of the gastrointestinal tract, which lives in trillions of gut microorganisms, in a healthy state, the host interacts with the gut microbiota and is symbiotic. The species Limosilactobacillus reuteri, Ligilactobacillus salivarius, and Lactobacillus johnsonii are indigenous gut [...] Read more.
As the critical component of the gastrointestinal tract, which lives in trillions of gut microorganisms, in a healthy state, the host interacts with the gut microbiota and is symbiotic. The species Limosilactobacillus reuteri, Ligilactobacillus salivarius, and Lactobacillus johnsonii are indigenous gut commensal bacteria that are mainly found in the digestive tracts. These three bacteria possess a variety of characteristics that reflect their ability to adapt to the gastrointestinal environment. Herein, we summarize the current progress of research on the probiotic properties of these strains in terms of their ability to protect against harmful pathogens, maintain intestinal health, and improve disease outcomes. These bacteria can impact the intestinal barrier function and enhance intestinal immunity through various mechanisms, such as upregulating the tight-junction protein expression and mucin secretion of intestinal epithelial cells, adjusting and balancing the gut microbiota, and blocking pro-inflammatory cytokine production. They have been shown to ameliorate intestinal inflammation in animal models and provide protective effects against various healthy issues in humans, including diarrhea, constipation, colorectal cancer, obesity, and liver diseases. However, the detailed mechanisms of certain strains remain unclear. Full article
(This article belongs to the Special Issue The Gut Microbiota—Its Role and Molecular Mechanisms in Nutritional Health)
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