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Nutrition, Gut Microbiota and Immunity
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Nutrition, Gut Microbiota and Immunity

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

Deadline for manuscript submissions: 31 August 2025 | Viewed by 15172

Special Issue Editor

Prof. Dr. Fang He

E-Mail Website
Guest Editor
Department of Nutrition and Food Hygiene, West China School of Public Health, Sichuan University, Chengdu, China
Interests: intestinal microbiology and immunity; probiotics and prebiotics; food microbiology and technology; nutrition, disease and public health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The human intestinal tract is colonized by trillions of diverse microbes, and most of them taxonomically belong to bacteria, which are organized as a complex human intestinal microbe ecosystem, well known as gut microbiota. Accumulating scientific evidence has well indicated that the gut microbiota might be a critical environmental factor that determines or influences the development and programing of human immunity. The dysbiosis of gut microbiota has been found among the important pathological features of the diseases/disorders characterized by immune dysfunction/deregulation such as allergy, IBS, IBD, etc. Nutrition can not only dynamically influence the structure of gut microbiota in quantity and quality but also alter/regulate its metabolic profile such as short-chain fatty acids, trimethylamine-N-oxide, lipopolysaccharides, and secondary bile acid. The recent studies indicate that nutrition can characteristically enhance/or mediate human immunity in a way that alters the gut microbiota. Nutritional interventions targeting the gut microbiota may be a new strategy that contributes to and promotes human health and well being.

This Special Issue on “Nutrition, Gut Microbiota and Immunity” aims to publish selected high-quality studies with a focus on specific aspects of nutrition, gut microbiota, and immunity. In particular, the studies (reviews and/or clinical or experimental studies) on the clinical effects, underlying mechanisms, and the related key functional compounds for nutrient intervention for human immunity that impact gut microbiota will be included.

Prof. Dr. Fang He
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 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • gut microbial metabolites 
  • immunity 
  • nutrient 
  • diet 
  • nutritional interventions

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Published Papers (7 papers)

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Research

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22 pages, 2973 KiB  
Article
Effects of Blueberry Consumption on Fecal Microbiome Composition and Circulating Metabolites, Lipids, and Lipoproteins in a Randomized Controlled Trial of Older Adults with Overweight or Obesity: The BEACTIVE Trial
by Kathryn N. Porter Starr, Margery A. Connelly, Jessica Wallis, Rebecca North, Qimin Zhang, Kuncheng Song, Jessica M. González-Delgado, Hayden N. Brochu, Crystal R. Icenhour, Lakshmanan K. Iyer, Marshall G. Miller, Kim M. Huffman, William E. Kraus and Connie W. Bales
Nutrients 2025, 17(7), 1200; https://doi.org/10.3390/nu17071200 - 29 Mar 2025
Viewed by 1084
Abstract
Background/Objectives: Generous consumption of phytonutrient-rich foods, including blueberries, provides benefits to multiple physiologic and metabolic systems. This study explored the potential that regular, generous blueberry intake could favorably modulate fecal microbiome composition in sedentary older (>60 years) men and women with overweight or [...] Read more.
Background/Objectives: Generous consumption of phytonutrient-rich foods, including blueberries, provides benefits to multiple physiologic and metabolic systems. This study explored the potential that regular, generous blueberry intake could favorably modulate fecal microbiome composition in sedentary older (>60 years) men and women with overweight or obesity (BMI ≥ 25 to 32 kg/m2). Methods: Participants (n = 55) were randomized to daily consumption of either lyophilized blueberry powder (equivalent to 1.5 cups of blueberries) or an indistinguishable placebo powder; both groups participated in weekly supervised exercise classes. Fecal samples were collected at 0 and 12 weeks and frozen. Following this, 16S rRNA gene sequencing was used to profile each participant’s fecal microbiome. Blood biomarkers of cardiometabolic health were measured via nuclear magnetic resonance spectroscopy (NMR) pre- and post-treatment. Results: Comparing the baseline and endpoint results for the blueberry (n = 15) and placebo (n = 19) groups, there were no significant overall compositional differences or differences in the level of diversity in the fecal microbiome. However, in subjects whose diet included blueberry powder, there was a significant enrichment (p = 0.049) in the relative abundance of Coriobacteriales incertae sedis, a taxonomic group of bacteria that facilitates the metabolism of dietary polyphenols. The placebo group exhibited significant reductions in total cholesterol, LDL-C, non-HDL-C, total LDL-P, large LDL-P, and ApoB, while the blueberry group exhibited significant reductions in total HDL-P and ApoA-I after 12 weeks compared to baseline. Conclusions: Generous blueberry consumption may upregulate the ability of the older human gut to utilize dietary polyphenols by altering the fecal microbiome. Longer, larger-scale studies with blueberries or blueberry powder are needed to observe improvements in cardiometabolic risk factors in older adults with overweight or obesity. Full article
(This article belongs to the Special Issue Nutrition, Gut Microbiota and Immunity)
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26 pages, 3405 KiB  
Article
A Data-Driven Approach to Enhance the Prediction of Bacteria–Metabolite Interactions in the Human Gut Microbiome Using Enzyme Encodings and Metabolite Structural Embeddings
by Gopal Srivastava and Michal Brylinski
Nutrients 2025, 17(3), 469; https://doi.org/10.3390/nu17030469 - 28 Jan 2025
Viewed by 945
Abstract
Background: The human gut microbiome is critical for host health by facilitating essential metabolic processes. Our study presents a data-driven analysis across 312 bacterial species and 154 unique metabolites to enhance the understanding of underlying metabolic processes in gut bacteria. The focus of [...] Read more.
Background: The human gut microbiome is critical for host health by facilitating essential metabolic processes. Our study presents a data-driven analysis across 312 bacterial species and 154 unique metabolites to enhance the understanding of underlying metabolic processes in gut bacteria. The focus of the study was to create a strategy to generate a theoretical (negative) set for binary classification models to predict the consumption and production of metabolites in the human gut microbiome. Results: Our models achieved median balanced accuracies of 0.74 for consumption predictions and 0.95 for production predictions, highlighting the effectiveness of this approach in generating reliable negative sets. Additionally, we applied a kernel principal component analysis for dimensionality reduction. The consumption model with a polynomial kernel, and the production model with a radial basis function with 32 reduced features, showed median accuracies of 0.58 and 0.67, respectively. This demonstrates that biological information can still be captured, albeit with some loss, even after reducing the number of features. Furthermore, our models were validated on six previously unseen cases, achieving five correct predictions for consumption and four for production, demonstrating alignment with known biological outcomes. Conclusions: These findings highlight the potential of integrating data-driven approaches with machine learning techniques to enhance our understanding of gut microbiome metabolism. This work provides a foundation for creating bacteria–metabolite datasets to enhance machine learning-based predictive tools, with potential applications in developing therapeutic methods targeting gut microbes. Full article
(This article belongs to the Special Issue Nutrition, Gut Microbiota and Immunity)
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21 pages, 1756 KiB  
Article
Association of Mucin-Degrading Gut Microbiota and Dietary Patterns with Colonic Transit Time in Constipation: A Secondary Analysis of a Randomized Clinical Trial
by Xuangao Wu, Hee-Jong Yang, Myeong-Seon Ryu, Su-Jin Jung, Kwangsu Ha, Do-Yeon Jeong and Sunmin Park
Nutrients 2025, 17(1), 138; https://doi.org/10.3390/nu17010138 - 31 Dec 2024
Cited by 1 | Viewed by 1489
Abstract
Background: The relationship between gut microbiota composition, lifestyles, and colonic transit time (CTT) remains poorly understood. This study investigated associations among gut microbiota profiles, diet, lifestyles, and CTT in individuals with subjective constipation. Methods: We conducted a secondary analysis of data from our [...] Read more.
Background: The relationship between gut microbiota composition, lifestyles, and colonic transit time (CTT) remains poorly understood. This study investigated associations among gut microbiota profiles, diet, lifestyles, and CTT in individuals with subjective constipation. Methods: We conducted a secondary analysis of data from our randomized clinical trial, examining gut microbiota composition, CTT, and dietary intake in baseline and final assessments of 94 participants with subjective constipation. Participants were categorized into normal-transit (<36 h) and slow-transit (≥36 h) groups based on CTT at baseline. Gut microbiota composition was measured using 16S rRNA sequencing, and dietary patterns were assessed through semi-quantitative food frequency questionnaires. Enterotype analysis, machine learning approaches, and metabolic modeling were employed to investigate microbiota–diet interactions. The constipated participants primarily belonged to Lachnospiraceae (ET-L). Results: The slow-transit group showed higher alpha diversity than the normal-transit group. Butyricicoccus faecihominis was abundant in the normal-transit group, while Neglectibacter timonensis, Intestinimonas massiliensis, and Intestinibacter bartlettii were abundant in the slow-transit group, which also had a higher abundance of mucin-degrading bacteria. Metabolic modeling predicted increased N-acetyl-D-glucosamine (GlcNAc), a mucin-derived metabolite, in the slow-transit group. Network analysis identified two microbial co-abundance groups (CAG3 and CAG9) significantly associated with transit time and dietary patterns. Six mucin-degrading species showed differential correlations with GlcNAc and a plant-based diet, particularly, including rice, bread, fruits and vegetables, and fermented beans. In conclusion, an increased abundance of mucin-degrading bacteria and their predicted metabolic products were associated with delayed CTT. Conclusion: These findings suggest dietary modulation of these bacterial populations as a potential therapeutic strategy for constipation. Moreover, our results reveal a potential immunometabolic mechanism where mucin-degrading bacteria and their metabolic interactions may influence intestinal transit, mucosal barrier function, and immune response. Full article
(This article belongs to the Special Issue Nutrition, Gut Microbiota and Immunity)
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Review

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19 pages, 630 KiB  
Review
Research Progress of Oral Immune Tolerance Mechanism Induced by Whey Protein
by Mao Lin, Qianqian Zhang and Yanjun Cong
Nutrients 2025, 17(9), 1517; https://doi.org/10.3390/nu17091517 (registering DOI) - 29 Apr 2025
Abstract
Cow milk allergy (CMA) is prevalently observed among infants and young children, exerting adverse effects on their growth and quality of life. Oral immune tolerance (OIT) is a more effective method for the prevention and treatment of CMA. The site of OIT is [...] Read more.
Cow milk allergy (CMA) is prevalently observed among infants and young children, exerting adverse effects on their growth and quality of life. Oral immune tolerance (OIT) is a more effective method for the prevention and treatment of CMA. The site of OIT is mainly in the gastrointestinal tract, so this article reviews the composition and structural characteristics of intestinal immune system, the molecular mechanisms of immune tolerance by regulatory T cells (Treg), dendritic cells, and gut microbiota. In addition, this paper summarizes the research progress of T cell epitope peptides of β-lactoglobulin and α-lactalbumin in whey protein hydrolysates. The mechanism of OIT induced by whey protein hydrolysate or whey protein combined with other anti-allergic components (phenolic compounds, probiotics, etc.) is overviewed to provide new ideas for the development of hypoallergenic infant formula. Full article
(This article belongs to the Special Issue Nutrition, Gut Microbiota and Immunity)
20 pages, 657 KiB  
Review
The Detrimental Impact of Ultra-Processed Foods on the Human Gut Microbiome and Gut Barrier
by Debora Rondinella, Pauline Celine Raoul, Eleonora Valeriani, Irene Venturini, Marco Cintoni, Andrea Severino, Francesca Sofia Galli, Vincenzina Mora, Maria Cristina Mele, Giovanni Cammarota, Antonio Gasbarrini, Emanuele Rinninella and Gianluca Ianiro
Nutrients 2025, 17(5), 859; https://doi.org/10.3390/nu17050859 - 28 Feb 2025
Cited by 2 | Viewed by 8160
Abstract
Ultra-processed foods (UPFs) have become a widely consumed food category in modern diets. However, their impact on gut health is raising increasing concerns. This review investigates how UPFs impact the gut microbiome and gut barrier, emphasizing gut dysbiosis and increased gut permeability. UPFs, [...] Read more.
Ultra-processed foods (UPFs) have become a widely consumed food category in modern diets. However, their impact on gut health is raising increasing concerns. This review investigates how UPFs impact the gut microbiome and gut barrier, emphasizing gut dysbiosis and increased gut permeability. UPFs, characterized by a high content of synthetic additives and emulsifiers, and low fiber content, are associated with a decrease in microbial diversity, lower levels of beneficial bacteria like Akkermansia muciniphila and Faecalibacterium prausnitzii, and an increase in pro-inflammatory microorganisms. These alterations in the microbial community contribute to persistent inflammation, which is associated with various chronic disorders including metabolic syndrome, irritable bowel syndrome, type 2 diabetes, and colorectal cancer. In addition, UPFs may alter the gut–brain axis, potentially affecting cognitive function and mental health. Dietary modifications incorporating fiber, fermented foods, and probiotics can help mitigate the effects of UPFs. Furthermore, the public needs stricter regulations for banning UPFs, along with well-defined food labels. Further studies are necessary to elucidate the mechanisms connecting UPFs to gut dysbiosis and systemic illnesses, thereby informing evidence-based dietary guidelines. Full article
(This article belongs to the Special Issue Nutrition, Gut Microbiota and Immunity)
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14 pages, 266 KiB  
Review
Gut over Mind: Exploring the Powerful Gut–Brain Axis
by Stefana-Maria Petrut, Alexandra Maria Bragaru, Alice Elena Munteanu, Adina-Diana Moldovan, Cosmin-Alec Moldovan and Elena Rusu
Nutrients 2025, 17(5), 842; https://doi.org/10.3390/nu17050842 - 28 Feb 2025
Cited by 1 | Viewed by 2295
Abstract
Background: The human gastrointestinal tract is home to a wide variety of microorganisms. For some decades now, bacteria known as probiotics have been added to various foods because of their beneficial effects for human health. Evidence indicates that probiotics significantly regulate gut microbiota, [...] Read more.
Background: The human gastrointestinal tract is home to a wide variety of microorganisms. For some decades now, bacteria known as probiotics have been added to various foods because of their beneficial effects for human health. Evidence indicates that probiotics significantly regulate gut microbiota, which is vital for digestion, metabolism, immune function, and mental health. Methods: We conducted a narrative review of available original research published in PubMed for the past ten years focusing on recent advancements that provide a thorough understanding of the relationship between the gastrointestinal system and the brain. Results: Recent advances in research have focused on the importance of gut microbiota in influencing mental health. The microbiota–gut–brain axis is a complex, bidirectional communication network linking the central nervous system and the gastrointestinal tract, which highlights how the gut and brain are deeply interconnected and influence each other in ways that affect our overall health, emotions, and behavior. This powerful link is a major area of research as scientists discover more about how gut health can impact mental well-being. Conclusions: A comprehensive understanding of microbiota composition and mechanisms involved in these interactions between the gut and the brain could shape future medical and therapeutic approaches. It would balance scientific explanation with clinical relevance, offering insights into how understanding the brain–gut axis can revolutionize our approach to treating mental health and gastrointestinal disorders. Full article
(This article belongs to the Special Issue Nutrition, Gut Microbiota and Immunity)
16 pages, 1143 KiB  
Review
Diet and Microbiota Modulation for Chronic Pouchitis: Evidence, Challenges, and Opportunities
by Pierluigi Puca, Angelo Del Gaudio, Guia Becherucci, Franco Sacchetti, Luigi Sofo, Loris Riccardo Lopetuso, Alfredo Papa, Giovanni Cammarota and Franco Scaldaferri
Nutrients 2024, 16(24), 4337; https://doi.org/10.3390/nu16244337 - 16 Dec 2024
Viewed by 1619
Abstract
Chronic pouchitis occurs in about 50% of patients undergoing a restorative proctocolectomy for ulcerative colitis. This affection represents a significant therapeutic challenge, particularly for symptomatic patients who do not respond to antibiotic treatments and biologic therapies. Several dietary approaches, including low FODMAP diets [...] Read more.
Chronic pouchitis occurs in about 50% of patients undergoing a restorative proctocolectomy for ulcerative colitis. This affection represents a significant therapeutic challenge, particularly for symptomatic patients who do not respond to antibiotic treatments and biologic therapies. Several dietary approaches, including low FODMAP diets and the Mediterranean diet, have shown promising results in improving symptoms and disease burden. The rationale for dietary intervention lies in the reduction in inflammation and modulation of gut microbiota. However, conflicting results and methodological heterogeneity jeopardize the transition of these approaches from the field of research to clinical practice. Together with a nutritional approach, innovative methods of microbiota modulation, including probiotics and fecal microbiota transplantation, are emerging as safe and effective strategies in managing chronic pouchitis. This narrative review analyzes recent advancements in nutritional therapies and microbiota modulation as innovative and complementary approaches for managing chronic pouchitis. After examining microbiota modulation strategies, specifically the effectiveness of probiotics, prebiotics, and fecal microbiota transplantation in restoring microbial diversity and their potential role in alleviating symptoms, the review assesses the available clinical evidence concerning dietary interventions and their impact on gut microbiota. A comprehensive understanding of interventions aimed at modulating the microbiota is crucial for enhancing the effectiveness of conventional therapies. Such strategies may lead to significant improvements in patients’ quality of life and their perception of the disease. However, the variability in microbiota composition, the use of restrictive diets, and the lack of standardized methods for evaluating these interventions remain significant challenges. Future research is essential to improve our understanding of the underlying mechanisms and optimize clinical application. Full article
(This article belongs to the Special Issue Nutrition, Gut Microbiota and Immunity)
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