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

Deadline for manuscript submissions: 30 September 2026 | Viewed by 7884

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Editors

Dr. Runan Zhao

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Guest Editor

1. School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
2. 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
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Wenjun Wang

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

Dr. Yini Liu

E-Mail Website
Guest Editor Assistant

Food Science Program, Division of Food, Nutrition & Exercise Sciences, University of Missouri, Columbia, MO 65211, USA
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-anonymized 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

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Published Papers (7 papers)

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Research

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20 pages, 6433 KB

Open AccessArticle

Identification and Characterization of Limosilactobacillus reuteri Strain S3 Isolated from Chicken and Its Protective Efficacy Against Avian Coccidiosis

by Nianyu Xue, Qianqian Feng, Dandan Liu, Weimin Cai, Yuxin Zhou, Zhaofeng Hou, Jinjun Xu and Jianping Tao

Microorganisms 2026, 14(8), 1659; https://doi.org/10.3390/microorganisms14081659 - 29 Jul 2026

Viewed by 271

Abstract

Limosilactobacillus reuteri is one of the common lactic acid bacteria in the chicken gastrointestinal tract. Our previous study revealed that L. reuteri abundance declined in White Leghorn chickens following infection with Eimeria tenella, E. maxima, and E. necatrix, suggesting a potential role of this species in gut homeostasis during coccidiosis. In this study, eight L. reuteri strains were isolated from the intestinal tract of White Leghorn chickens. Strain S3 was selected as the most promising candidate after screening for acid and bile tolerance, adhesion ability, antagonism against pathogens. Oral administration of S3 strain at dose of 4 × 10⁷ CFU/bird, 1.2 × 10⁸ CFU/bird or 2 × 10⁸ CFU/bird for 18 days improved average daily gain (ADG) in both White Leghorn chickens and Suqin laying hens. The ADG value in groups treated with 4 × 10⁷ CFU/bird was significantly higher compared to that in the control group (p < 0.05). This treatment did not cause adverse effects on hepatic or renal function, but significantly increased the thymus index in both breeds and the levels of total protein and globulin in Suqin laying hens (p < 0.05). S3 strain also modulated gut microbiota composition in White Leghorn chickens, promoting beneficial lactobacilli colonization in the jejunum and achieving persistent colonization in the cecum. S3 strain selectively increased the proportion of CD3⁺CD4⁺ T lymphocytes in peripheral blood of Suqin laying hens. The anticoccidial efficacy of S3 strain was evaluated in Suqin laying hens challenged with E. tenella, E. maxima, and E. necatrix. The results showed that S3 strain alleviated clinical signs, reduced lesion scores, decreased oocyst output, and attenuated body weight loss. Anticoccidial index (ACI) values were 130.67, 148.06, and 163.40 for E. tenella, E. maxima, and E. necatrix infection, respectively. These results suggest that L. reuteri S3 is a safe chicken-derived probiotic with immunomodulatory and anticoccidial properties, and may serve as a feed additive for coccidiosis control in poultry production. Full article

(This article belongs to the Special Issue Gut Microbes and Probiotics)

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20 pages, 3001 KB

Open AccessArticle

Evaluation of Limosilactobacillus reuteri ATCC PTA 6127 Reveals Multilayered Antimicrobial and Epithelial Barrier-Supportive Effects in a Canine Epithelial Model

by Josh Walker, Akila Rekima, Andreea Cornelia Udrea, Katrine Bie Larsen, Adrian Schwarzenberg, Steffen Yde Bak, Niels Christensen, Svetlana Gerdes, Weiqing Zeng, Ashley Hibberd and Chong Shen

Microorganisms 2026, 14(7), 1422; https://doi.org/10.3390/microorganisms14071422 - 29 Jun 2026

Viewed by 365

Abstract

Good canine gastrointestinal health depends on the suppression of enteric pathogens and maintenance of epithelial barrier integrity. Limosilactobacillus reuteri ATCC PTA 6127 (Lr6127) is a dog-derived probiotic, but evidence supporting its functional properties remains limited. Here, we evaluated the antimicrobial and epithelial-supportive effects of Lr6127 using a canine epithelial cell model. Cell-free supernatant (CFS) from Lr6127 significantly inhibited the growth of canine-relevant pathogens, including Enterotoxigenic Escherichia coli (52.0 ± 1.3%), Clostridium perfringens (54.0 ± 2.7%), and Salmonella enterica subsp. enterica serovar Typhimurium (48.6 ± 1.2%), compared with the medium control (p < 0.0001). Pathogen inhibition increased in a dose-dependent manner with increasing CFS concentration. Untargeted metabolomic analysis revealed enrichment of multiple antimicrobial-associated metabolites, indicating a multi-component profile consistent with pathogen suppression, with genomic analysis supporting the aromatic amino acid-derived metabolite findings. In addition, viable Lr6127 significantly reduced the epithelial adhesion of all the tested pathogens (p < 0.01). Beyond direct antimicrobial effects, Lr6127 CFS promoted epithelial wound healing at later time points, accompanied by the coordinated modulation of proteins associated with cytoskeletal remodeling and barrier repair. Collectively, these findings support the idea that Lr6127 is associated with antimicrobial and epithelial-related effects, highlighting its potential to contribute to epithelial function under controlled in vitro conditions. Full article

(This article belongs to the Special Issue Gut Microbes and Probiotics)

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22 pages, 2432 KB

Open AccessArticle

Effects of Tannic Acid on Immune Function and Gut Microbiota in Brandt’s Voles (Lasiopodomys brandtii)

by Jin Li, Kunying Zhou, Di Xu, Yunqi Liu, Yu Sun and Deli Xu

Microorganisms 2026, 14(3), 577; https://doi.org/10.3390/microorganisms14030577 - 3 Mar 2026

Cited by 1 | Viewed by 775

Abstract

The present study investigates the effects of tannic acid (TA) on body composition, immune function, and gut microbiota in Brandt’s voles (Lasiopodomys brandtii); analyzes the gut microbiota–immune parameter associations during their response to plant secondary metabolites; and provides a theoretical basis for understanding their adaptive mechanisms. Thirty-three female Brandt’s voles were randomly divided into four groups and intragastrically administered distilled water (control group) or TA at doses of 300, 600, and 1200 mg·kg⁻¹·d⁻¹ for 9 weeks. The results showed that TA had no significant effect on body mass, body composition (including subcutaneous, retroperitoneal, mesenteric, and perigonadal fat, as well as total fat mass), immune organ weights, or cellular immune responses in Brandt’s voles. However, high-dose TA (1200 mg·kg⁻¹·d⁻¹) significantly reduced the serum anti-KLH IgG titers in a dose-dependent manner, indicating selective impairment of humoral immunity. High-dose TA (1200 mg·kg⁻¹·d⁻¹) also decreased the alpha diversity of the gut microbiota, with lower Chao1, Observed features, and Shannon indices compared to the control and low-dose (300 mg·kg⁻¹·d⁻¹) groups. Beta diversity analysis indicated that high-dose TA (1200 mg·kg⁻¹·d⁻¹) altered the overall gut microbiota structure, while taxonomic analyses revealed a decrease in Desulfobacterota and an increase in several gut-associated taxa, including Firmicutes, Clostridia, Lachnospirales, and Lachnospiraceae. In conclusion, high-dose TA (1200 mg·kg⁻¹·d⁻¹) induced significant changes in the gut microbiota and selectively suppressed humoral immunity. However, other immune parameters and growth-related measures remained unaffected. These findings suggest a potential role of gut microbial adjustments in modulating host responses to dietary TA and contribute to knowledge of the tolerance mechanisms in this species. Full article

(This article belongs to the Special Issue Gut Microbes and Probiotics)

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22 pages, 11279 KB

Open AccessArticle

Lactobacillus rhamnosus GG Alleviates Post-Weaning Stress-Induced Intestinal Barrier Damage and Inflammation by Promoting Intestinal Health and Modulating the Gut Microbiota in Piglets

by Gaohuan Hou, Hongbin Deng, Lingliang Zhou, Yang Liu, Weiqin Li, Weifen Li and Qi Wang

Microorganisms 2026, 14(2), 410; https://doi.org/10.3390/microorganisms14020410 - 9 Feb 2026

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Abstract

The aim of this study is to investigate oral administration of L. rhamnosus GG (LGG) in early life on the growth performance, diarrhea, intestinal health, and microbiota of post-weaning piglets. Ninety-six newborn piglets were randomly divided into two groups. Piglets were orally administered with 2 mL of 10% sterile skim milk or 2 mL of 10% sterile skim milk suspended with viable LGG (1 × 10⁸ CFU/mL). Results showed that compared with the control group, oral administration of LGG in early life slightly decreased diarrhea incidence. Furthermore, LGG supplementation maintained the intestinal barrier integrity (HE, DAO) and reduced the generation of the inflammatory response. 16S rRNA sequencing showed that LGG modulated the colon microbiota composition of piglets by increasing the relative abundance of Bifidobacterium, Helicobacter, Mucispirillum, and Dorea. Metabolomic study suggested that LGG substantially influenced the intestinal metabolic profile, particularly compounds associated with the biosynthesis of unsaturated fatty acids. The metabolic alterations were closely linked to the enhancement of the microbial community makeup. The analysis of jejunum RNA sequencing indicated that, in comparison to the CON group, LGG significantly downregulated various immune-related signaling pathways, especially the PI3K/AKT pathways. Correlation analysis of microbiota, metabolism, and genes uncovered a substantial association between the taxa enhanced by LGG and the critical genes in the PI3K/AKT signaling pathways. The coculture system of LGG and intestinal organoids revealed that LGG alleviated TNF-α induced injury through inhibiting the PI3K/AKT signaling pathway. Overall, the integrated analysis of multiple omics approaches revealed that LGG reduced post-weaning induced intestinal injury through the regulation of gut microbiota, modification of metabolic profiles, reinforcement of the intestinal barrier, and downregulation of the PI3K/AKT signaling pathway. Full article

(This article belongs to the Special Issue Gut Microbes and Probiotics)

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9 pages, 803 KB

Open AccessArticle

Heat-Killed Enterococcus faecalis EF-2001 Promotes Systemic Th1-Skewed Immune Activation Without Detectable Reduction of Influenza Viral Load in Mice

by Takahisa Ohashi, Mao Hagihara, Nobuhiro Asai, Yuka Yamagishi and Hiroshige Mikamo

Microorganisms 2026, 14(2), 316; https://doi.org/10.3390/microorganisms14020316 - 29 Jan 2026

Viewed by 986

Abstract

Heat-killed Enterococcus faecalis EF-2001 (EF-2001) is a postbiotic preparation reported to modulate host immunity. However, its specific impact on host immune responses and virological outcomes during the early phase of influenza infection remains insufficiently characterized. Female BALB/c mice received oral EF-2001 (16 mg/kg/day) for either 4 days or 14 days prior to intranasal inoculation with influenza A/H3N2 (A/Aichi/2/68). On day 2 post-infection, splenic T-cell subsets (CD3⁺, CD4⁺, CD8⁺) were quantified by flow cytometry. Cytokines released from PMA/ionomycin-stimulated splenocytes were measured using a cytometric bead array assay to assess functional polarization. Lung viral titers (TCID₅₀) and interferon-α (IFN-α) concentrations were assessed to evaluate local antiviral efficacy. EF-2001 administration significantly increased the proportions of splenic CD3⁺ T cells, including both CD4⁺ and CD8⁺ subsets, compared to controls. The 14-day pretreatment regimen significantly enhanced IFN-γ production while reducing IL-10, IL-4, and IL-2 secretion, consistent with a distinct systemic Th1-skewed immune activation. In contrast to these systemic effects, EF-2001 did not significantly reduce lung viral titers (difference < 0.2 log₁₀ TCID₅₀) and did not increase lung IFN-α concentrations at day 2 post-infection. Oral EF-2001 pretreatment promoted systemic immune activation characterized by T-cell expansion and a Th1-biased cytokine profile. However, this systemic priming showed no detectable antiviral effect on lung viral burden at the early evaluation time point. EF-2001 may be better positioned as an adjunctive immunomodulatory approach rather than a direct antiviral agent, warranting further studies that include clinical outcomes and multi-time-point antiviral and mucosal immune assessments. Full article

(This article belongs to the Special Issue Gut Microbes and Probiotics)

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13 pages, 3108 KB

Open AccessArticle

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 607

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 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)

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15 pages, 832 KB

Open AccessReview

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

Cited by 3 | Viewed by 2625

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 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)

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