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The Role of Microbiota in Nutrition and Diet: An Ever-Evolving Relationship

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

Deadline for manuscript submissions: 25 August 2025 | Viewed by 38610

Special Issue Editor


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Guest Editor
Department of Medicine, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
Interests: gut microbiota; proteomics; metabolomics; cardiovascular diseases; nutrition

Special Issue Information

Dear Colleagues,

The relationship between microbiota, diet, and nutrition is crucial for human health. The intestinal microbiota, composed of billions of microorganisms, plays a fundamental role in digestion, the immune system, and nutrient synthesis. Diet significantly influences the composition and diversity of the gut microbiota. Consuming foods rich in fiber, fruits, vegetables, and probiotics promotes the growth of beneficial bacteria, while a diet high in saturated fats and sugars can imbalance the microbiota, increasing the risk of metabolic diseases and gastrointestinal disorders.

The microbiota also influences the absorption of nutrients, such as vitamins and minerals, directly impacting an individual's nutritional status. For example, certain gut bacteria participate in the production of vitamins B and K, essential for various bodily functions. In turn, nutrition affects the health of the microbiota, as a balanced and varied diet provides the necessary nutrients to maintain a healthy microbial ecosystem.

This symbiotic relationship between microbiota, diet, and nutrition underscores the importance of adopting healthy eating habits to favor bacterial diversity and promote balance within the body, thereby contributing to disease prevention and optimal health maintenance.

Dr. Luís Collado-Yurrita
Guest Editor

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Keywords

  • microbiota
  • diet
  • nutrition
  • allergy
  • irritable colon
  • oral biofilm
  • butyrate
  • probiotics

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Published Papers (8 papers)

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Research

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14 pages, 218 KiB  
Article
Probiotics and Synbiotics Administered to Young Infants: Perceptions and Acceptability Amongst Carers and Healthcare Workers in Western Kenya
by Mary Iwaret Otiti, Florence Achieng Were, Sevim Zaim, Helen Nabwera, Simon Kariuki and Stephen Allen
Nutrients 2025, 17(3), 495; https://doi.org/10.3390/nu17030495 - 29 Jan 2025
Viewed by 1299
Abstract
Background/Objectives: A contributory factor to childhood undernutrition is poor gut health occurring within the first 6–12 weeks of life despite exclusive breastfeeding. Pro/synbiotic administration may protect gut health. A qualitative study was conducted amongst mothers/carers and healthcare workers (HCWs) to explore their perceptions [...] Read more.
Background/Objectives: A contributory factor to childhood undernutrition is poor gut health occurring within the first 6–12 weeks of life despite exclusive breastfeeding. Pro/synbiotic administration may protect gut health. A qualitative study was conducted amongst mothers/carers and healthcare workers (HCWs) to explore their perceptions and the acceptability of pro/synbiotics administration in early life. Methods: This study was nested within a randomised, open, clinical trial of pro/synbiotics with 32 doses administered under supervision to infants between ages 0 and 5 months in western Kenya. Semi-structured interviews were conducted with 14 mothers/carers, 12 Peer Mothers and 7 healthcare workers (HCWs) selected by purposive critical and key informant sampling. Interviews were transcribed and analysed using a thematic coding framework. Results: The satisfaction with the pro/synbiotic administration was very high amongst all three groups. Commonly perceived benefits included protection from diseases, healthy growth of the infant and improved appetite. The main barriers were working mothers and other commitments making it difficult to stick to scheduled administration visits, adverse judgement and opinions in the community, and a lack of engagement from fathers. Insights were gained into different means of administering pro/synbiotics to young infants. Triangulation of the findings of the mothers/carers with HCWs showed that most identified motivations and challenges were similar. Conclusions: Pro/synbiotic administration was well accepted by the mothers/carers and HCWs and generally perceived to have health benefits. The administration of pro/synbiotics by the mothers/carers themselves to their infants may be feasible and overcome logistical challenges. Greater efforts to sensitise and engage fathers and communities would likely be critical for a community-based program. Full article
16 pages, 484 KiB  
Article
Is the Mediterranean Low Fodmap Diet Effective in Managing Irritable Bowel Syndrome Symptoms and Gut Microbiota? An Innovative Research Protocol
by Arezina N. Kasti, Konstantinos Katsas, Konstantinos Petsis, Sophia Lambrinou, Kalliopi D. Synodinou, Aliki Kapetani, Kerry Louise Smart, Maroulla D. Nikolaki, Panagiotis Halvatsiotis, Konstantinos Triantafyllou and Jane G. Muir
Nutrients 2024, 16(11), 1592; https://doi.org/10.3390/nu16111592 - 23 May 2024
Cited by 5 | Viewed by 3244
Abstract
Introduction: Irritable bowel syndrome (IBS) symptoms can be effectively managed with the low FODMAP diet. However, its efficacy in reducing inflammation is not yet proven. On the contrary, the Mediterranean diet has anti-inflammatory properties with proven efficacy in treating chronic low-grade inflammation-related diseases. [...] Read more.
Introduction: Irritable bowel syndrome (IBS) symptoms can be effectively managed with the low FODMAP diet. However, its efficacy in reducing inflammation is not yet proven. On the contrary, the Mediterranean diet has anti-inflammatory properties with proven efficacy in treating chronic low-grade inflammation-related diseases. Aim: To publicly share our protocol evaluating the efficacy of the Mediterranean low-FODMAP (MED-LFD) versus NICE recommendations (British National Institute for Health and Care Excellence) diet in managing IBS symptoms and quality of life. Materials and Methods: Participants meeting the Rome IV criteria will be randomly assigned to MED-LFD or NICE recommendations and they will be followed for six months. Efficacy, symptom relief, quality of life and mental health will be assessed using validated questionnaires. In addition, fecal samples will be analyzed to assess gut microbiota, and to measure branched and short-chain fatty acids, and volatile organic compounds (metabolic byproducts from bacteria). Expected results and discussion: By publicly sharing this clinical study protocol, we aim to improve research quality in the field of IBS management by allowing for peer review feedback, preventing data manipulation, reducing redundant research efforts, mitigating publication bias, and empowering patient decision-making. We expect that this protocol will show that MED-LFD can effectively alleviate IBS symptoms and it will provide pathophysiology insights on its efficacy. The new dietary pattern that combines the LFD and the MED approaches allows for the observation of the synergistic action of both diets, with the MED’s anti-inflammatory and prebiotic properties enhancing the effects of the LFD while minimizing its limitations. Identifier in Clinical Trials: NCT03997708 Full article
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21 pages, 8970 KiB  
Article
Lactobacillus delbrueckii subsp. bulgaricus Alleviates Acute Injury in Hypoxic Mice
by Ke Song, Hui Ling, Linlin Wang, Peijun Tian, Xing Jin, Jianxin Zhao, Wei Chen, Gang Wang and Yujing Bi
Nutrients 2024, 16(10), 1465; https://doi.org/10.3390/nu16101465 - 13 May 2024
Cited by 3 | Viewed by 3058
Abstract
Acute mountain sickness (AMS) is a common ailment in high-altitude areas caused by the body’s inadequate adaptation to low-pressure, low-oxygen environments, leading to organ edema, oxidative stress, and impaired intestinal barrier function. The gastrointestinal tract, being the first to be affected by ischemia [...] Read more.
Acute mountain sickness (AMS) is a common ailment in high-altitude areas caused by the body’s inadequate adaptation to low-pressure, low-oxygen environments, leading to organ edema, oxidative stress, and impaired intestinal barrier function. The gastrointestinal tract, being the first to be affected by ischemia and hypoxia, is highly susceptible to injury. This study investigates the role of Lactobacillus delbrueckii subsp. bulgaricus in alleviating acute hypoxic-induced intestinal and tissue damage from the perspective of daily consumed lactic acid bacteria. An acute hypoxia mouse model was established to evaluate tissue injury, oxidative stress, inflammatory responses, and intestinal barrier function in various groups of mice. The results indicate that strain 4L3 significantly mitigated brain and lung edema caused by hypoxia, improved colonic tissue damage, and effectively increased the content of tight junction proteins in the ileum, reducing ileal permeability and alleviating mechanical barrier damage in the intestines due to acute hypoxia. Additionally, 4L3 helped to rebalance the intestinal microbiota. In summary, this study found that Lactobacillus delbrueckii subsp. bulgaricus strain 4L3 could alleviate acute intestinal damage caused by hypoxia, thereby reducing hypoxic stress. This suggests that probiotic lactic acid bacteria that exert beneficial effects in the intestines may alleviate acute injury under hypoxic conditions in mice, offering new insights for the prevention and treatment of AMS. Full article
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15 pages, 2819 KiB  
Article
Effects of Gluten on Gut Microbiota in Patients with Gastrointestinal Disorders, Migraine, and Dermatitis
by Ismael San Mauro Martín, Sara López Oliva, Elena Garicano Vilar, Guerthy Melissa Sánchez Niño, Bruno F. Penadés, Ana Terrén Lora, Sara Sanz Rojo and Luis Collado Yurrita
Nutrients 2024, 16(8), 1228; https://doi.org/10.3390/nu16081228 - 20 Apr 2024
Cited by 4 | Viewed by 3880
Abstract
As gluten may trigger gastrointestinal disorders (GIDs), its presence or absence in the diet can change the diversity and proportion of gut microbiota. The effects of gluten after six weeks of a double-blind, placebo-controlled intervention with a gluten-free diet (GFD) were studied in [...] Read more.
As gluten may trigger gastrointestinal disorders (GIDs), its presence or absence in the diet can change the diversity and proportion of gut microbiota. The effects of gluten after six weeks of a double-blind, placebo-controlled intervention with a gluten-free diet (GFD) were studied in participants with GIDs suffering from migraines and atopic dermatitis (n = 46). Clinical biomarkers, digestive symptoms, stool, the Migraine Disability Assessment questionnaire, and zonulin levels were analyzed. Next-generation sequencing was used to amplify the 16S rRNA gene of bacteria and the internal transcribed spacer (ITS) regions of fungi. The GFD increased Chao1 fungal diversity after the intervention, while the fungal composition showed no changes. Bacterial diversity and composition remained stable, but a positive association between bacterial and fungal Chao1 diversity and a negative association between Dothideomycetes and Akkermansia were observed. GIDs decreased in both groups and migraines improved in the placebo group. Our findings may aid the development of GID treatment strategies. Full article
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17 pages, 5274 KiB  
Article
A Free Amino Acid Diet Alleviates Colorectal Tumorigenesis through Modulating Gut Microbiota and Metabolites
by Yang-Meng Yu, Gui-Fang Li, Yi-Lin Ren, Xin-Yi Xu, Zheng-Hong Xu, Yan Geng and Yong Mao
Nutrients 2024, 16(7), 1040; https://doi.org/10.3390/nu16071040 - 3 Apr 2024
Cited by 2 | Viewed by 2749
Abstract
Colorectal cancer (CRC), a major global health concern, may be influenced by dietary protein digestibility impacting gut microbiota and metabolites, which is crucial for cancer therapy effectiveness. This study explored the effects of a casein protein diet (CTL) versus a free amino acid [...] Read more.
Colorectal cancer (CRC), a major global health concern, may be influenced by dietary protein digestibility impacting gut microbiota and metabolites, which is crucial for cancer therapy effectiveness. This study explored the effects of a casein protein diet (CTL) versus a free amino acid (FAA)-based diet on CRC progression, gut microbiota, and metabolites using carcinogen-induced (AOM/DSS) and spontaneous genetically induced (ApcMin/+ mice) CRC mouse models. Comprehensive approaches including 16s rRNA gene sequencing, transcriptomics, metabolomics, and immunohistochemistry were utilized. We found that the FAA significantly attenuated CRC progression, evidenced by reduced colonic shortening and histopathological alterations compared to the CTL diet. Notably, the FAA enriched beneficial gut bacteria like Akkermansia and Bacteroides and reversed CRC-associated dysbiosis. Metabolomic analysis highlighted an increase in ornithine cycle metabolites and specific fatty acids, such as Docosapentaenoic acid (DPA), in FAA-fed mice. Transcriptomic analysis revealed that FAA up-regulated Egl-9 family hypoxia inducible factor 3 (Egln 3) and downregulated several cancer-associated pathways including Hippo, mTOR, and Wnt signaling. Additionally, DPA was found to significantly induce EGLN 3 expression in CRC cell lines. These results suggest that FAA modulate gut microbial composition, enhance protective metabolites, improve gut barrier functions, and inhibit carcinogenic pathways. Full article
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Review

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29 pages, 2290 KiB  
Review
Beyond the Gut: Unveiling Butyrate’s Global Health Impact Through Gut Health and Dysbiosis-Related Conditions: A Narrative Review
by Arda Erkan Kalkan, Mona N. BinMowyna, António Raposo, Md Faruque Ahmad, Faiyaz Ahmed, Abdullah Y. Otayf, Conrado Carrascosa, Ariana Saraiva and Sercan Karav
Nutrients 2025, 17(8), 1305; https://doi.org/10.3390/nu17081305 - 9 Apr 2025
Viewed by 1615
Abstract
Short-chain fatty acids (SCFAs), mainly produced by gut microbiota through the fermentation process of dietary fibers and proteins, are crucial to human health, with butyrate, a famous four-carbon SCFA, standing out for its inevitably regulatory impact on both gut and immune functions. Within [...] Read more.
Short-chain fatty acids (SCFAs), mainly produced by gut microbiota through the fermentation process of dietary fibers and proteins, are crucial to human health, with butyrate, a famous four-carbon SCFA, standing out for its inevitably regulatory impact on both gut and immune functions. Within this narrative review, the vital physiological functions of SCFAs were examined, with emphasis on butyrate’s role as an energy source for colonocytes and its ability to enhance the gut barrier while exhibiting anti-inflammatory effects. Knowledge of butyrate synthesis, primarily generated by Firmicutes bacteria, can be influenced by diets with specifically high contents of resistant starches and fiber. Butyrate can inhibit histone deacetylase, modulate gene expression, influence immune functionality, and regulate tight junction integrity, supporting the idea of its role in gut barrier preservation. Butyrate possesses systemic anti-inflammatory properties, particularly, its capacity to reduce pro-inflammatory cytokines and maintain immune homeostasis, highlighting its therapeutic potential in managing dysbiosis and inflammatory diseases. Although butyrate absorption into circulation is typically minimal, its broader health implications are substantial, especially regarding obesity and type 2 diabetes through its influence on metabolic regulation and inflammation. Furthermore, this narrative review thoroughly examines butyrate’s growing recognition as a modulator of neurological health via its interaction with the gut–brain axis. Additionally, butyrate’s neuroprotective effects are mediated through activation of specific G-protein-coupled receptors, such as FFAR3 and GPR109a, and inhibition of histone deacetylases (HDACs). Research indicates that butyrate can alleviate neurological disorders, including Alzheimer’s, Parkinson’s, autism spectrum disorder, and Huntington’s disease, by reducing neuroinflammation, enhancing neurotransmitter modulation, and improving histone acetylation. This focus will help unlock its full therapeutic potential for metabolic and neurological health, rather than exclusively on its well-known benefits for gut health, as these are often interconnected. Full article
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31 pages, 3064 KiB  
Review
Unraveling the Gut Microbiota: Implications for Precision Nutrition and Personalized Medicine
by Alessio Abeltino, Duaa Hatem, Cassandra Serantoni, Alessia Riente, Michele Maria De Giulio, Marco De Spirito, Flavio De Maio and Giuseppe Maulucci
Nutrients 2024, 16(22), 3806; https://doi.org/10.3390/nu16223806 - 6 Nov 2024
Cited by 14 | Viewed by 6382
Abstract
Recent studies have shown a growing interest in the complex relationship between the human gut microbiota, metabolism, and overall health. This review aims to explore the gut microbiota–host association, focusing on its implications for precision nutrition and personalized medicine. The objective is to [...] Read more.
Recent studies have shown a growing interest in the complex relationship between the human gut microbiota, metabolism, and overall health. This review aims to explore the gut microbiota–host association, focusing on its implications for precision nutrition and personalized medicine. The objective is to highlight how gut microbiota modulate metabolic and immune functions, contributing to disease susceptibility and wellbeing. The review synthesizes recent research findings, analyzing key studies on the influence of gut microbiota on lipid and carbohydrate metabolism, intestinal health, neurobehavioral regulation, and endocrine signaling. Data were drawn from both experimental and clinical trials examining microbiota–host interactions relevant to precision nutrition. Our findings highlight the essential role of gut microbiota-derived metabolites in regulating host metabolism, including lipid and glucose pathways. These metabolites have been found to influence immune responses and gut barrier integrity. Additionally, the microbiota impacts broader physiological processes, including neuroendocrine regulation, which could be crucial for dietary interventions. Therefore, understanding the molecular mechanisms of dietary–microbiota–host interactions is pivotal for advancing personalized nutrition strategies. Tailored dietary recommendations based on individual gut microbiota compositions hold promise for improving health outcomes, potentially revolutionizing future healthcare approaches across diverse populations. Full article
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22 pages, 1735 KiB  
Review
The Role of Gut Microbiome in Sleep Quality and Health: Dietary Strategies for Microbiota Support
by Monika Sejbuk, Adam Siebieszuk and Anna Maria Witkowska
Nutrients 2024, 16(14), 2259; https://doi.org/10.3390/nu16142259 - 13 Jul 2024
Cited by 7 | Viewed by 15342
Abstract
Dietary components, including dietary fiber, unsaturated fatty acids, and polyphenols, along with meal timing and spacing, significantly affect the microbiota’s capacity to produce various metabolites essential for quality sleep and overall health. This review explores the role of gut microbiota in regulating sleep [...] Read more.
Dietary components, including dietary fiber, unsaturated fatty acids, and polyphenols, along with meal timing and spacing, significantly affect the microbiota’s capacity to produce various metabolites essential for quality sleep and overall health. This review explores the role of gut microbiota in regulating sleep through various metabolites such as short-chain fatty acids, tryptophan, serotonin, melatonin, and gamma-aminobutyric acid. A balanced diet rich in plant-based foods enhances the production of these sleep-regulating metabolites, potentially benefiting overall health. This review aims to investigate how dietary habits affect gut microbiota composition, the metabolites it produces, and the subsequent impact on sleep quality and related health conditions. Full article
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