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Nutrients
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Advances in Gut Microbial Genomics and Metabolomics in Human Health
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Advances in Gut Microbial Genomics and Metabolomics in Human Health

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

Deadline for manuscript submissions: closed (25 July 2025) | Viewed by 1487

Special Issue Editors

Dr. Hea-jong Chung

E-Mail Website
Guest Editor
Gwanju Center, Korea Basic Science Institute, Gwanju 61715, Republic of Korea
Interests: microbiome; gut microbiome; brain diseases; neurobiology; probiotics
Special Issues, Collections and Topics in MDPI journals
Dr. Ji-Seon Ahn

E-Mail Website
Guest Editor
Korea Basic Science Institute, Gwangju, Republic of Korea
Interests: gut microbiome; fecal microbiome; neuroprotection; neurobiology; neuropathology

Special Issue Information

Dear Colleagues,

This Special Issue will explore the latest advancements in gut microbial genomics and metabolomics, highlighting their critical role in human health. The human microbiome is integral to various physiological processes, including digestion, metabolism, and immune function, with disruptions linked to diseases such as obesity, diabetes, cardiovascular disorders, and neurological conditions. Recent innovations in genomics and metabolomics have deepened our understanding of microbial diversity and the metabolites that microbes produce, providing insights into their impacts on health and disease. We welcome contributions that address the molecular mechanisms behind gut microbiome dysbiosis, the role of microbial metabolites in metabolic and immune regulation, and how these insights can lead to new therapeutic approaches for chronic diseases. Studies investigating the effects of diet, lifestyle, and environmental factors on microbiome composition, as well as the potential of microbiome-based therapies, are also encouraged. This Special Issue will provide a comprehensive platform for the latest research on microbial genomics and metabolomics, advancing our understanding of the microbiome’s role in human health and disease prevention.

Dr. Hea-jong Chung
Dr. Ji-Seon Ahn
Guest Editors

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 microbiome
  • metabolomics
  • health
  • metagenomics
  • disease

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Published Papers (2 papers)

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Research

20 pages, 4259 KB  
Article
Human Gut Microbiota Profiles Related to Mediterranean and West African Diets and Association with Blastocystis Subtypes
by Lorenzo Antonetti, Federica Berrilli, Marina Cardellini, Massimo Federici and Rossella D’Alfonso
Nutrients 2025, 17(18), 2950; https://doi.org/10.3390/nu17182950 - 13 Sep 2025
Viewed by 303
Abstract
Background/Objectives: The effects of geographical origin, alongside age, diet, and drug treatments, on the gut microbiota have not been thoroughly analyzed in African countries. Furthermore, eukaryotic components, including Blastocystis, the most common intestinal protozoan worldwide, require further investigation. This study compares [...] Read more.
Background/Objectives: The effects of geographical origin, alongside age, diet, and drug treatments, on the gut microbiota have not been thoroughly analyzed in African countries. Furthermore, eukaryotic components, including Blastocystis, the most common intestinal protozoan worldwide, require further investigation. This study compares the gut microbiota of Italian subjects with that of two African groups to examine the influence of dietary patterns and the effects of Blastocystis presence and subtypes. Methods: Three cohorts of healthy subjects (Italians residing in Rome, Africans residing in the Côte d’Ivoire, and Africans living in Italy) were compared by sequencing the V3-V4 hypervariable regions of the 16S rDNA gene. Taxa abundance and associations with typical West African and Italian foods were determined using DESeq2. Co-abundant genera were identified with a weighted correlation network analysis (WGCNA). Blastocystis subtypes were determined and correlated with the microbial composition in the three groups. Results: Distinct microbial taxa were associated with specific foods, including palm oil, Cube Maggi, sunflower oil, and olive oil. A Mediterranean diet consumed for over two years did not alter the abundance of Faecalibacterium and Dorea in the Africans living in Italy compared with Africans living in Côte d’Ivoire, whereas differences were observed in the abundance of some Prevotella-9, Bacteroides, and Lachnospiraceae OTUs. Significant associations were identified between palm oil and Subdoligranulum, Cube Maggi and Dorea, sunflower oil and the Ruminococcus torques group, and olive oil and Faecalibacterium. Concerning Blastocystis, alpha and beta diversity analysis showed a significant separation between carriers and non-carriers. Conclusions: This study provides the first comparative analysis of gut microbiota composition between individuals from Côte d’Ivoire and Italians focusing on the influence of distinct dietary patterns. Full article
(This article belongs to the Special Issue Advances in Gut Microbial Genomics and Metabolomics in Human Health)
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25 pages, 3717 KB  
Article
A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Attenuates Hypergravity-Induced Disruptions to the Microbiome in Female Mice
by Robert S. Thompson, Shelby Hopkins, Tel Kelley, Christopher G. Wilson, Michael J. Pecaut and Monika Fleshner
Nutrients 2025, 17(15), 2417; https://doi.org/10.3390/nu17152417 - 24 Jul 2025
Viewed by 776
Abstract
Background/Objectives: Environmental stressors, including spaceflight and altered gravity, can negatively affect the symbiotic relationship between the gut microbiome and host health. Dietary prebiotics, which alter components of the gut microbiome, show promise as an effective way to mitigate the negative impacts of stressor [...] Read more.
Background/Objectives: Environmental stressors, including spaceflight and altered gravity, can negatively affect the symbiotic relationship between the gut microbiome and host health. Dietary prebiotics, which alter components of the gut microbiome, show promise as an effective way to mitigate the negative impacts of stressor exposure. It remains unknown, however, if the stress-protective effects of consuming dietary prebiotics will extend to chronic altered-gravity exposure. Methods: Forty female C57BL/6 mice consumed either a control diet or a prebiotic diet containing galactooligosaccharides (GOS) and polydextrose (PDX) for 4 weeks, after which half of the mice were exposed to 3 times the gravitational force of Earth (3g) for an additional 4 weeks. Fecal microbiome samples were collected weekly for 8 weeks, sequenced, and analyzed using 16S rRNA gene sequencing. Terminal physiological endpoints, including immune and red blood cell characteristics, were collected at the end of the study. Results: The results demonstrate that dietary prebiotic consumption altered the gut microbial community structure through changes to β-diversity and multiple genera across time. In addition, consuming dietary prebiotics reduced the neutrophil-to-lymphocyte ratio (NLR) and increased red blood cell distribution width (RDW-CV). Importantly, the prebiotic diet prevented the impacts of altered-gravity on β-diversity and the bloom of problematic genera, such as Clostridium_sensu_stricto_1 and Turicibacter. Furthermore, several prebiotic diet-induced genera-level changes were significantly associated with several host physiological changes induced by 3g exposure. Conclusions: These data demonstrate that the stress-protective potential of consuming dietary prebiotics extends to environmental stressors such as altered gravity, and, potentially, spaceflight. Full article
(This article belongs to the Special Issue Advances in Gut Microbial Genomics and Metabolomics in Human Health)
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