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Nutrients
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Probiotics, Postbiotics, Gut Microbiota and Gastrointestinal Health
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Probiotics, Postbiotics, Gut Microbiota and Gastrointestinal Health

A special issue of Nutrients (ISSN 2072-6643). This special issue belongs to the section "Prebiotics, Probiotics and Postbiotics".

Deadline for manuscript submissions: 15 July 2026 | Viewed by 10663

Special Issue Editor

Prof. Dr. Fei Liu

E-Mail Website
Guest Editor
Key Laboratory of Dairy Science, Ministry of Education, Food College, Northeast Agricultural University, Harbin, China
Interests: lactic acid bacteria taxonomy; probiotic metabolism and fermentation engineering; probiotics and intestinal microecology regulation; stabilization and delivery system for probiotics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The human gastrointestinal tract contains a complex microbial ecosystem that plays a key role in maintaining host health through dynamic interactions with metabolic, immune, and neurological systems. Disruptions in this delicate balance, termed dysbiosis, are increasingly linked to inflammatory bowel diseases, functional GI disorders, obesity, and even extra-intestinal conditions such as nervous system and autoimmune diseases. Emerging research highlights the critical contributions of probiotics and postbiotics in modulating gut microbiota composition and function, thereby influencing gastrointestinal homeostasis. As live microorganisms, probiotics act through multifaceted mechanisms, including enhancing mucosal barrier function via tight junction protein modulation, the competitive exclusion of pathogens, and the production of bioactive metabolites. Postbiotics, in contrast, exert immunomodulatory and anti-inflammatory effects independent of microbial viability. Crucially, probiotics and postbiotics both have the ability to shape gut microbiota ecology by enriching commensal taxa.

We are pleased to invite you to contribute works with cutting-edge methodologies, including multi-omics integration, synthetic biology, and microbiota engineering, to unravel causal relationships between microbial communities and host physiology. This Special Issue aims to explore the molecular mechanisms underlying probiotic–host interactions, the therapeutic potential of postbiotics, and innovative strategies with which to restore gut microbiota balance in disease states. We aspire to synthesize different insights in order to utilize microbial resources for combating gastrointestinal disorders globally and foster the development of next-generation biotherapeutics. In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  • Molecular cross-talk mechanisms governing probiotic–host interactions.
  • Emerging therapeutic applications of postbiotic metabolites.
  • Novel intervention strategies for gut microbiota modulation in pathological conditions.

I look forward to receiving your contributions.

Prof. Dr. Fei Liu
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. Nutrients is an international peer-reviewed open access semimonthly 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 2900 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

  • postbiotics
  • gut microbiota
  • gastrointestinal health
  • gastrointestinal homeostasis
  • fermented foods
  • synthetic biology

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Published Papers (5 papers)

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Research

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19 pages, 2743 KB  
Article
Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source
by Jacqueline Rehner, Madline Gund, Sören L. Becker, Matthias Hannig, Stefan Rupf, Jörn M. Schattenberg, Andreas Keller, the IMAGINE Consortium, Leidy-Alejandra G. Molano and Verena Keller
Nutrients 2025, 17(22), 3527; https://doi.org/10.3390/nu17223527 - 11 Nov 2025
Viewed by 743
Abstract
Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen [...] Read more.
Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m2) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen’s d. Results: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; p = 9 × 10−3). Several taxa showed an opposite directionality between oral and gut sites, including Streptococcus salivarius and Bifidobacterium longum, indicating site-specific associations. Notably, Actinomyces sp. and Streptococcus sp. exhibited promising effect sizes as diagnostic markers. Conclusions: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity. Full article
(This article belongs to the Special Issue Probiotics, Postbiotics, Gut Microbiota and Gastrointestinal Health)
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26 pages, 663 KB  
Article
Probiotic Sheep Milk: Physicochemical Properties of Fermented Milk and Viability of Bacteria Under Simulated Gastrointestinal Conditions
by Małgorzata Pawlos, Katarzyna Szajnar and Agata Znamirowska-Piotrowska
Nutrients 2025, 17(21), 3340; https://doi.org/10.3390/nu17213340 - 24 Oct 2025
Cited by 1 | Viewed by 1001
Abstract
Background/Objectives: Within the spectrum of lactic acid bacteria, Lacticaseibacillus casei and Lactobacillus johnsonii are of particular technological and nutritional significance. Protein fortification of fermented dairy systems offers dual benefits: it improves product quality while enhancing probiotic resilience. Supplementary proteins supply bioavailable nitrogen and [...] Read more.
Background/Objectives: Within the spectrum of lactic acid bacteria, Lacticaseibacillus casei and Lactobacillus johnsonii are of particular technological and nutritional significance. Protein fortification of fermented dairy systems offers dual benefits: it improves product quality while enhancing probiotic resilience. Supplementary proteins supply bioavailable nitrogen and peptides that stimulate bacterial metabolism and contribute to a viscoelastic gel matrix that buffers cells against gastric acidity and bile salts. The aim of this study was to clarify the functional potential of such formulations by assessing probiotic survival under in vitro digestion simulating oral, gastric, and intestinal phases. Methods: Sheep milk was fermented with L. casei 431 or L. johnsonii LJ in the presence of whey protein isolate (WPI), soy protein isolate (SPI), or pea protein isolate (PPI) at concentrations of 1.5% and 3.0%. Physicochemical parameters (pH, titratable acidity, color, syneresis), organoleptic properties, and microbiological counts were evaluated. The viability of L. casei and L. johnsonii was determined at each digestion stage, and probiotic survival rates were calculated. Results: Samples with L. johnsonii consistently exhibited lower pH values compared to L. casei. Across both bacterial strains, the addition of 1.5% protein isolate more effectively limited syneresis than 3.0%, regardless of protein type. Samples fortified with WPI at 1.5% (JW1.5) and 3.0% (JW3.0) were rated highest by the panel, demonstrating smooth, homogeneous textures without grittiness. The greatest bacterial survival (>70%) was observed in WPI-fortified samples (JW1.5, JW3.0) and in SPI-fortified JS3. Conclusions: Protein isolates of diverse origins are suitable for the enrichment of fermented sheep milk, with 1.5% supplementation proving optimal. Such formulations maintained desirable fermentation dynamics and, in most cases, significantly improved the survival of L. casei and L. johnsonii under simulated gastrointestinal conditions, underscoring their potential in the development of functional probiotic dairy products. Full article
(This article belongs to the Special Issue Probiotics, Postbiotics, Gut Microbiota and Gastrointestinal Health)
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29 pages, 6122 KB  
Article
Lacticaseibacillus paracasei L21 and Its Postbiotics Ameliorate Ulcerative Colitis Through Gut Microbiota Modulation, Intestinal Barrier Restoration, and HIF1α/AhR-IL-22 Axis Activation: Combined In Vitro and In Vivo Evidence
by Jingru Chen, Linfang Zhang, Yuehua Jiao, Xuan Lu, Ning Zhang, Xinyi Li, Suo Zheng, Bailiang Li, Fei Liu and Peng Zuo
Nutrients 2025, 17(15), 2537; https://doi.org/10.3390/nu17152537 - 1 Aug 2025
Cited by 6 | Viewed by 3197
Abstract
Background: Ulcerative colitis (UC), characterized by chronic intestinal inflammation, epithelial barrier dysfunction, and immune imbalance demands novel ameliorative strategies beyond conventional approaches. Methods: In this study, the probiotic properties of Lactobacillus paracaseiL21 (L. paracaseiL21) and its ability to ameliorate [...] Read more.
Background: Ulcerative colitis (UC), characterized by chronic intestinal inflammation, epithelial barrier dysfunction, and immune imbalance demands novel ameliorative strategies beyond conventional approaches. Methods: In this study, the probiotic properties of Lactobacillus paracaseiL21 (L. paracaseiL21) and its ability to ameliorate colitis were evaluated using an in vitro lipopolysaccharide (LPS)-induced intestinal crypt epithelial cell (IEC-6) model and an in vivo dextran sulfate sodium (DSS)-induced UC mouse model. Results: In vitro, L. paracaseiL21 decreased levels of pro-inflammatory cytokines (TNF-α, IL-1β, IL-8) while increasing anti-inflammatory IL-10 levels (p < 0.05) in LPS-induced IEC-6 cells, significantly enhancing the expression of tight junction proteins (ZO-1, occludin, claudin-1), thereby restoring the intestinal barrier. In vivo, both viable L. paracaseiL21 and its heat-inactivated postbiotic (H-L21) mitigated weight loss, colon shortening, and disease activity indices, concurrently reducing serum LPS and proinflammatory mediators. Interventions inhibited NF-κB signaling while activating HIF1α/AhR pathways, increasing IL-22 and mucin MUC2 to restore goblet cell populations. Gut microbiota analysis showed that both interventions increased the abundance of beneficial gut bacteria (Lactobacillus, Dubococcus, and Akkermansia) and improved faecal propanoic acid and butyric acid levels. H-L21 uniquely exerted an anti-inflammatory effect, marked by the regulation of Dubosiella, while L. paracaseiL21 marked by the Akkermansia. Conclusions: These results highlight the potential of L. paracaseiL21 as a candidate for the development of both probiotic and postbiotic formulations. It is expected to provide a theoretical basis for the management of UC and to drive the development of the next generation of UC therapies. Full article
(This article belongs to the Special Issue Probiotics, Postbiotics, Gut Microbiota and Gastrointestinal Health)
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21 pages, 506 KB  
Article
Fermented Milk Supplemented with Sodium Butyrate and Inulin: Physicochemical Characterization and Probiotic Viability Under In Vitro Simulated Gastrointestinal Digestion
by Katarzyna Szajnar, Małgorzata Pawlos, Magdalena Kowalczyk, Julita Drobniak and Agata Znamirowska-Piotrowska
Nutrients 2025, 17(13), 2249; https://doi.org/10.3390/nu17132249 - 7 Jul 2025
Cited by 1 | Viewed by 3167
Abstract
Background/Objectives: Probiotics are increasingly recognized for their role in managing gastrointestinal disorders through modulation of gut microbiota. Restoring microbial balance remains a therapeutic challenge. Recent strategies combine probiotics, inulin, and sodium butyrate as synergistic agents for gut health. This study aimed to evaluate [...] Read more.
Background/Objectives: Probiotics are increasingly recognized for their role in managing gastrointestinal disorders through modulation of gut microbiota. Restoring microbial balance remains a therapeutic challenge. Recent strategies combine probiotics, inulin, and sodium butyrate as synergistic agents for gut health. This study aimed to evaluate the effects of milk supplementation with inulin and sodium butyrate on physicochemical properties, sensory characteristics, and the survival of selected probiotic strains during in vitro simulated gastrointestinal digestion. Methods: Fermented milk samples were analyzed for color, pH, titratable acidity, and syneresis. A trained sensory panel evaluated aroma, texture, and acceptability. Samples underwent a standardized in vitro digestion simulating oral, gastric, and intestinal phases. Viable probiotic cells were counted before digestion and at each stage, and survival rates were calculated. Results: Physicochemical and sensory attributes varied depending on probiotic strain and supplementation. Inulin and the inulin–sodium butyrate combination influenced syneresis and acidity. Lacticaseibacillus casei 431 and Lactobacillus johnsonii LJ samples showed the highest viable counts before digestion. Two-way ANOVA confirmed that probiotic strain, supplementation type, and their interactions significantly affected bacterial survival during digestion (p < 0.05). Conclusions: The addition of inulin and sodium butyrate did not impair probiotic viability under simulated gastrointestinal conditions. The effects on product characteristics were strain-dependent (Bifidobacterium animalis subsp. lactis BB-12, L. casei 431, L. paracasei L26, L. acidophilus LA-5, L. johnsonii LJ). These findings support the use of inulin–butyrate fortification in dairy matrices to enhance the functional potential of probiotic foods targeting gut health. Full article
(This article belongs to the Special Issue Probiotics, Postbiotics, Gut Microbiota and Gastrointestinal Health)
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Review

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13 pages, 982 KB  
Review
The Impact of Diet on the Fecal Microbiota Transplantation Success in Patients with Gastrointestinal Diseases—A Literature Review
by Natalia Komorniak, Katarzyna Gaweł, Anna Deskur, Jan Pawlus and Ewa Stachowska
Nutrients 2025, 17(20), 3314; https://doi.org/10.3390/nu17203314 - 21 Oct 2025
Viewed by 1960
Abstract
Background: Fecal microbiota transplantation (FMT) is a therapeutic method involving the administration of appropriately prepared feces from a healthy donor to the gastrointestinal tract of a recipient. This literature review aims to summarize and critically evaluate the available evidence on the impact of [...] Read more.
Background: Fecal microbiota transplantation (FMT) is a therapeutic method involving the administration of appropriately prepared feces from a healthy donor to the gastrointestinal tract of a recipient. This literature review aims to summarize and critically evaluate the available evidence on the impact of different dietary patterns and nutrients on the efficacy of FMT. Methods: The present literature review focuses on the impact of diet on the gut microbiota in the context of the effectiveness of fecal microbiota transplantation. A literature review was conducted based on the PubMed Database. Results: More and more data confirm the close link between diet and gut microbiota and suggest that proper nutrition before and after FMT may support the effectiveness of this procedure. It appears that increased fiber intake significantly delays the loss of diversity in the transplanted microbiota, thereby enhancing the beneficial clinical effects following FMT. Additionally, the use of an anti-inflammatory components in the diet combination with FMT could be effective in achieving clinical remission in patients with ulcerative colitis. Conclusions: Based on the literature review, it appears that the most optimal nutritional model (through its beneficial effect on the composition of the gut microbiota, short-chain fatty acids production, and intestinal barrier integrity) to support the effectiveness of FMT is an anti-inflammatory diet rich in dietary fiber (for both the donor and the recipient). Full article
(This article belongs to the Special Issue Probiotics, Postbiotics, Gut Microbiota and Gastrointestinal Health)
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