Human Gut Microbiome, Diets and Health

A Special Issue of Microorganisms (ISSN 2076-2607) belonging to the section "Gut Microbiota".

Deadline for manuscript submissions: closed (31 October 2025) | Viewed by 13634

Editors


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Guest Editor
Laboratory of Integrative Cancer Immunology, NCI/NIH, Bethesda, MD 20892, USA
Interests: human oral and gut microbiome; antibiotic-resistant bacteria; Gramnegative bacteria; anaerobes; effects of probiotics and antibiotics; LPS; horizontal gene transfer; plasmids; NGS

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Guest Editor
Harvard Medical School, University of Harvard, Boston, MA, 02114, USA
Interests: antibacterial activity; veterinary microbiology

Special Issue Information

Dear Colleagues,

The human gastrointestinal tract harbors a diversity of bacteria, viruses, fungi, and protozoa acquired early in life. The microbiota is a complex and dynamic ecosystem that plays a crucial role in human health and disease. The gut microbiota composition changes between populations based on diet, lifestyle, and geographic location. Diet impacts the composition and diversity of the gut microbiota and is essential for maintaining gut health and overall well-being. Different diets and eating patterns can influence bacterial diversity in the gut, while an imbalanced diet combined with an unhealthy lifestyle can have long-lasting effects. A high-fiber diet and fermented foods with probiotics may benefit the gut microbiome and support gut health. In contrast, a high consumption of processed foods, particularly those characteristic of the low-fiber, high-sugar Western diet, is associated with reduced microbial diversity. This poor dietary pattern increases the risks of obesity, cardiovascular disease, metabolic syndrome, and cancer, highlighting the importance of dietary choices in maintaining overall health. Thus, a balanced diet can reduce the incidence of chronic health conditions associated with poor gut health. Studying the ecology and interactions between a host and its microbiota promises profound insights into human health, with potential implications for the future prevention and treatment of a wide range of diseases.

This Special Issue will compile a collection of articles on the relationship between diet, the gut microbiome, and human health. It will offer new perspectives on how dietary patterns influence the gut microbiome and, consequently, human health. As the Guest Editor, I invite you to submit research articles, review articles, and short communications focusing on the interplay between diet and the gut microbiome. Topics of interest include but are not limited to the effects of various diets on microbial diversity, the role of prebiotics and probiotics, the impact of fiber intake, and the mechanisms by which diet-induced changes in the microbiota affect metabolic and immune health.

Dr. Miriam R. Fernandes
Dr. Carolina Dos Anjos
Guest Editors

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Keywords

  • gut microbiota
  • human nutrition
  • diet
  • probiotics and prebiotics
  • fermented food
  • gut health
  • metabolites
  • microbiota–host interactions

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Published Papers (4 papers)

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Research

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19 pages, 4854 KB  
Article
Dietary Effects, Age, and Urban–Rural Dynamics in Shaping Gut Microbiota of Elderly Vietnamese: A Cross-Sectional Study
by Adel Hamdi, Le Van Truong, Vu Thi Hien, Phuong Anh Nguyen, Thi Bach Duong Hoang, Charmaine Lloyd, Rajaraman Eri, Dragana Stanley, Dong Van Quyen and Thi Thu Hao Van
Microorganisms 2025, 13(12), 2803; https://doi.org/10.3390/microorganisms13122803 - 9 Dec 2025
Cited by 1 | Viewed by 1489
Abstract
Aging is associated with alterations in gut microbiota, yet the combined effects of geography and diet remain underexplored in elderly populations. This study investigated the gut microbiota of 227 healthy Vietnamese individuals aged ≥60 years, stratified by select urban and rural residence in [...] Read more.
Aging is associated with alterations in gut microbiota, yet the combined effects of geography and diet remain underexplored in elderly populations. This study investigated the gut microbiota of 227 healthy Vietnamese individuals aged ≥60 years, stratified by select urban and rural residence in both Hanoi and Thanh Hoa provinces, and across three age groups (60–69, 70–79, ≥80 years). Dietary patterns were collected and recorded for each participant. 16S rRNA gene sequencing revealed significant differences in microbial diversity and composition associated with geographical location (urban, rural) and age. Urban participants in Hanoi exhibited higher richness and greater abundance of health-associated genera, including Bifidobacterium, Fusicatenibacter, and Blautia, likely reflecting more diverse plant-based diets. In contrast, rural participants in Thanh Hoa showed enrichment of beneficial butyrate-producing genera such as Fusicatenibacter, Roseburia, Lachnospira and Blautia, possibly linked to traditional diets rich in freshwater fish and fermented foods. Participants aged 70–79 years displayed reduced microbial richness compared to other age groups. Age-related reductions in Roseburia, Veillonella, and Prevotella were also observed. These findings highlight how geography, diet, and aging shape the gut microbiota and may guide microbiota-targeted dietary strategies to promote healthy aging. Full article
(This article belongs to the Special Issue Human Gut Microbiome, Diets and Health)
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17 pages, 1602 KB  
Article
Genome Analysis of the Multidrug-Resistant Campylobacter coli BCT3 of the Sequence Type (ST) 872 Isolated from a Pediatric Diarrhea Case
by Konstantinos Papadimitriou, Anastasios Ioannidis, Aleksandra Slavko, Genovefa Chronopoulou, Nektarios Marmaras, Anastasia Pangalis, Elisavet Olntasi, Niki Vassilaki, Efthymia Ioanna Koufogeorgou, Iris Kolida, Dimitrios Theodoridis and Stylianos Chatzipanagiotou
Microorganisms 2025, 13(6), 1420; https://doi.org/10.3390/microorganisms13061420 - 18 Jun 2025
Viewed by 2109
Abstract
Campylobacter jejuni and Campylobacter coli are the two main campylobacter species that cause foodborne campylobacteriosis. Recent studies have reported that Campylobacter spp. are prone to developing resistance to antibiotics commonly used for their treatment, with many C. coli strains identified as multidrug-resistant. This [...] Read more.
Campylobacter jejuni and Campylobacter coli are the two main campylobacter species that cause foodborne campylobacteriosis. Recent studies have reported that Campylobacter spp. are prone to developing resistance to antibiotics commonly used for their treatment, with many C. coli strains identified as multidrug-resistant. This study presents the results of the whole-genome sequencing analysis of the multidrug-resistant C. coli strain BCT3 isolated in Greece from a stool specimen of a pediatric patient presenting with diarrhea. The strain was isolated using selective culture media and, based on antimicrobial susceptibility tests, was found to be resistant to ciprofloxacin, tetracycline, erythromycin, azithromycin, clarithromycin, and doxycycline. To further characterize it, we performed whole-genome sequencing, which identified strain BCT3 as C. coli. Moreover, multilocus sequence typing assigned the BCT3 to the sequence type (ST) 872, belonging to clonal complex ST-828. The presence of multiple virulence genes revealed its pathogenic potential. The detection of antimicrobial resistance genes and mutated alleles was indicative of its resistance to fluoroquinolones, macrolides, and tetracyclines, supporting the observed phenotype. To our knowledge, this is the first reported clinical case of such a multidrug-resistant C. coli strain in Greece. Full article
(This article belongs to the Special Issue Human Gut Microbiome, Diets and Health)
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30 pages, 3648 KB  
Article
Fecal Microbiome and Metabolomic Profiles of Mixed-Fed Infants Are More Similar to Formula-Fed than Breastfed Infants
by Mei Wang, Negin Valizadegan, Christopher J. Fields and Sharon M. Donovan
Microorganisms 2025, 13(1), 166; https://doi.org/10.3390/microorganisms13010166 - 14 Jan 2025
Cited by 8 | Viewed by 5918
Abstract
Many infants consume both human milk and infant formula (mixed-fed); however, few studies have investigated how mixed feeding affects the gut microbiome composition and metabolic profiles compared to exclusive breastfeeding or formula feeding. Herein, how delivery mode and early nutrition affect the microbiome [...] Read more.
Many infants consume both human milk and infant formula (mixed-fed); however, few studies have investigated how mixed feeding affects the gut microbiome composition and metabolic profiles compared to exclusive breastfeeding or formula feeding. Herein, how delivery mode and early nutrition affect the microbiome and metabolome of 6-week-old infants in the STRONG Kids2 cohort was investigated. Fecal samples were collected from exclusively breastfed (BF; n = 25), formula-fed (FF; n = 25) or mixed-fed (MF; n = 25) participants. Within each feeding group, infants were either delivered vaginally (VD; n = 13) or by Cesarean section (CS; n = 12). Feeding mode affects the fecal microbiome diversity, composition, and functional potential, as well as metabolomic profiles regardless of delivery mode. Alpha and beta diversity of MF differed from that of BF (p < 0.05) but were comparable to FF infants. Functional analyses have shown 117 potential metabolic pathways differed between BF and FF, 112 between BF and MF, and 8 between MF and FF infants (p < 0.05, q < 0.10). Fecal metabolomic profiles of MF and FF clustered together and separated from BF infants. In total, 543 metabolites differed between BF and FF, 517 between BF and MF, and 3 between MF and FF (p < 0.05, q < 0.10). Delivery mode affected overall microbial composition (p = 0.022) at the genus level and 24 potential functional pathways, with 16 pathways being higher in VD than CS infants (p < 0.05, q < 0.10). Metabolomic analysis identified 47 differential metabolites between CS and VD, with 39 being lower in CS than VD (p < 0.05, q < 0.10). In summary, fecal microbiota composition and function and metabolite profiles of 6-week-old MF infants are closer to FF than BF infants. Full article
(This article belongs to the Special Issue Human Gut Microbiome, Diets and Health)
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Review

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29 pages, 942 KB  
Review
A Review of Global Patterns in Gut Microbiota Composition, Health and Disease: Locating South Africa in the Conversation
by Nombulelo Mntambo, Thilona Arumugam, Ashiq Pramchand, Kamlen Pillay and Veron Ramsuran
Microorganisms 2025, 13(12), 2831; https://doi.org/10.3390/microorganisms13122831 - 12 Dec 2025
Cited by 5 | Viewed by 2496
Abstract
The gut microbiota plays an essential role in human health through its contributions to immune regulation, metabolism, pathogen defence and disease susceptibility. Despite this significance, most gut microbiome research remains disproportionately focused on high-income countries, resulting in a limited and underrepresented view of [...] Read more.
The gut microbiota plays an essential role in human health through its contributions to immune regulation, metabolism, pathogen defence and disease susceptibility. Despite this significance, most gut microbiome research remains disproportionately focused on high-income countries, resulting in a limited and underrepresented view of global microbial diversity. This bias is evident in Africa, where populations, including those in South Africa, show unique combinations of genetic variation, dietary patterns and environmental exposures that are insufficiently captured in current datasets but offer opportunities to uncover novel insights into microbial evolution and its influences on health across diverse settings. In response to this gap, this review synthesises global patterns in gut microbiota composition and diversity while situating South African findings within this broader context. We examine evidence across microbial domains, including bacteria, fungi, viruses, archaea, protozoa and helminths, and highlight the impact of dietary transitions and environmental exposures on microbial community structure. Although still emerging, research on the gut microbiome of South African populations consistently reports contrasts between rural and urban populations, with rural groups enriched in fibre-fermenting and anti-inflammatory taxa, whereas urban communities often exhibit reduced diversity and features of dysbiosis linked to Westernisation. However, limited sample sizes, heterogeneous methodologies and absence of multi-omic approaches constrain robust interpretation. These lacunae in current knowledge emphasise the urgent need for large-scale, longitudinal studies that reflect South Africa’s demographic and geographic diversity. Strengthening this evidence will not only help identify microbial signatures linked to modifiable lifestyle factors but will also guide nutrition, prevention and screening programmes to improve health in African populations. Full article
(This article belongs to the Special Issue Human Gut Microbiome, Diets and Health)
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