Gut Microbes and Probiotics

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

Deadline for manuscript submissions: 31 January 2026 | Viewed by 1034

Special Issue Editors

College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
Interests: single-cell encapsulation of probiotics; targeted functional food creation; food ingredient stabilization and nutritional delivery systems; natural polymer materials; food packaging

E-Mail Website
Guest Editor
College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
Interests: novel approaches for food engineering; hydrocolloids; emulsions; protein processing; sonoprocessing; food packaging
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor Assistant
School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
Interests: gut microbes and health; functional probiotic resource discovery; functional mechanisms of probiotic analysis

Special Issue Information

Dear Colleagues,

We are pleased to introduce this Special Issue on “Gut Microbes and Probiotics”, which presents recent advances in probiotic development, microbe–host interactions, and their roles in gut health.

The human gut microbiota plays a crucial role in maintaining host health through the metabolism of nutrients, regulation of the immune system, and defense against pathogens. Probiotics help sustain intestinal homeostasis and modulate immune responses. Recently, growing attention has been focused on the complex interactions between gut microbes and the host, particularly on the beneficial effects of probiotics and their metabolites.

This Special Issue aims to collect high-quality original research articles and reviews exploring the impact of probiotics on gut health. Topics of interest include the development of probiotic strains, the mechanisms by which probiotics maintain intestinal health, and the effects of their metabolites—such as short-chain fatty acids, indole derivatives, cell wall components, and exopolysaccharides—on gut health. We also welcome studies focusing on the protection, stabilization, and targeted delivery of probiotics, including microencapsulation, biomaterial-based carriers, controlled release formulations, and single-cell surface modifications, which are critical for maintaining probiotic viability and functionality during gastrointestinal transit.

Submissions employing in vitro models, in vivo experiments, clinical trials, or multi-omics approaches are encouraged. This Special Issue provides a timely platform for advancing the scientific understanding of gut microbiota and probiotics, as well as their translational potential in nutrition and health.

Dr. Runan Zhao
Prof. Dr. Wenjun Wang
Guest Editors

Dr. Yini Liu
Guest Editor Assistant

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. Microorganisms 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 2700 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 microbe
  • probiotics
  • host–microbe interactions
  • microbiome-based interventions
  • microencapsulation
  • targeted delivery system

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 (2 papers)

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

Research

Jump to: Review

13 pages, 3108 KB  
Article
Analysis of Intestinal Microbiota Differences and Functional Prediction Between Sichuan-Tibetan Black Pigs and Landrace Pigs
by Lichun Jiang, Yi Qing, Kaiyuan Huang, Huiling Huang, Chengmin Li and Yanci Li
Microorganisms 2026, 14(1), 258; https://doi.org/10.3390/microorganisms14010258 - 22 Jan 2026
Viewed by 44
Abstract
This study aimed to investigate the structural differences and functional potential of the gut microbiota between Sichuan-Tibetan black pigs (n = 5) and Landrace pigs (n = 5) under identical rearing conditions. Fecal samples were collected and subjected to 16S rRNA [...] Read more.
This study aimed to investigate the structural differences and functional potential of the gut microbiota between Sichuan-Tibetan black pigs (n = 5) and Landrace pigs (n = 5) under identical rearing conditions. Fecal samples were collected and subjected to 16S rRNA gene sequencing followed by comprehensive bioinformatics analysis. The results revealed 963 and 910 operational taxonomic units (OTUs) in Sichuan-Tibetan black pigs and Landrace pigs, respectively, with 808 OTUs shared between the two breeds. While both breeds shared Firmicutes, Bacteroidota, and Proteobacteria as the dominant phyla, significant compositional differences were observed at the genus level. Sichuan-Tibetan black pigs exhibited higher abundance of Escherichia-Shigella, Streptococcus, Prevotella, Parabacteroides, and Collinsella, whereas Landrace pigs were enriched in Bacteroides. Alpha diversity analysis showed no significant differences in Shannon, Simpson, or ACE indices, though the Chao index differed markedly between the two groups. Beta diversity analysis (PCoA and NMDS) confirmed distinct microbial community structures between the breeds. Functional prediction analysis demonstrated that metabolic pathways dominated in both groups, but with notable functional differentiation: the microbiota of Sichuan-Tibetan black pigs showed significant enrichment in biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and amino acid biosynthesis; whereas, Landrace pigs were characterized by enhanced carbon and energy metabolism pathways. Additionally, BugBase phenotype prediction revealed significant differences in stress tolerance, cell wall properties, and oxygen utilization capabilities between the two groups. These findings provide valuable insights into the breed-specific characteristics of gut microbiota in swine and establish a foundation for further research on host-microbe interactions and their implications for animal health and nutrition. Full article
(This article belongs to the Special Issue Gut Microbes and Probiotics)
Show Figures

Figure 1

Review

Jump to: Research

15 pages, 832 KB  
Review
Gastrointestinal Journey of Human Milk Oligosaccharides: From Breastfeeding Origins to Functional Roles in Adults
by Yosuke Komatsu, Megumi Furuichi and Takeshi Kokubo
Microorganisms 2026, 14(1), 29; https://doi.org/10.3390/microorganisms14010029 - 22 Dec 2025
Viewed by 519
Abstract
Human milk oligosaccharides (HMOs) are the third most abundant solid component in human milk and play crucial roles in shaping the gut microbiome and promoting infant health. Although their functions during infancy are well established, emerging evidence suggests that HMOs exert region-specific effects [...] Read more.
Human milk oligosaccharides (HMOs) are the third most abundant solid component in human milk and play crucial roles in shaping the gut microbiome and promoting infant health. Although their functions during infancy are well established, emerging evidence suggests that HMOs exert region-specific effects throughout the gastrointestinal tract, extending their benefits beyond early life. This review summarizes current findings on HMO activity in the oral cavity, stomach, small intestine, and large intestine, focusing on their microbiota-modulating, barrier-enhancing, and immunoregulatory effects. In the oral cavity, HMOs inhibit pathogen adhesion and biofilm formation, maintaining oral homeostasis. In the stomach, fucosylated and sialylated HMOs act as soluble decoy receptors, preventing Helicobacter pylori infection. In the small intestine, HMOs strengthen epithelial integrity, regulate inflammation, and promote nutrient absorption. In the large intestine, they serve as selective prebiotics for beneficial microbes, enhancing short-chain fatty acid production and improving barrier function. Although preclinical and clinical studies demonstrate their safety and efficacy, further research is required to elucidate their mechanisms in adults. Overall, HMOs represent multifunctional bioactive glycans with promising applications for gastrointestinal health across all ages. Full article
(This article belongs to the Special Issue Gut Microbes and Probiotics)
Show Figures

Graphical abstract

Back to TopTop