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Microorganisms
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Advances in Diet–Host–Gut Microbiome Interactions
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Advances in Diet–Host–Gut Microbiome Interactions

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbiomes".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 5419

Special Issue Editor

Dr. Yancong Zhang

E-Mail Website
Guest Editor
Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
Interests: microbiome; microbial genomics; meta-omics; microbiome–host interaction; microbiome–diet interaction; food science

Special Issue Information

Dear Colleagues,

The gut microbiome plays a vital role in influencing host health and disease by influencing digestion, nutrient absorption, metabolism, and immune function. Dietary components directly shape the composition and function of the gut microbiota, which in turn impacts various aspects of host physiology and susceptibility to diseases. There is growing interest in the role of functional foods, probiotics, prebiotics, and synbiotics in modulating gut microbiota composition and activity. In this context, studying the interactions among diet, host, and the gut microbiome is essential to understanding the intricate balance between dietary intake, the gut microbiota, and overall health outcomes. Unraveling the complexities of these interactions offers new avenues for promoting health and preventing disease through personalized nutrition and microbiome-targeted interventions.

As the Guest Editor of this Special Issue, I would like to invite you to submit perspective articles, original research articles, review articles, and short communications on various aspects of new mechanism insights into interplays among the diet, gut microbiome, and host, innovations in methodologies and technologies for studying diet–host–microbiome interactions, and advances in personalized nutrition approaches targeting the gut microbiota for health promotion and disease prevention.

Dr. Yancong Zhang
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. Microorganisms is an international peer-reviewed open access monthly 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 2700 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
  • diet
  • food
  • nutrition
  • dysbiosis
  • host–microbe interactions
  • microbial bioactive
  • multi-omics
  • microbial therapy
  • personalized nutrition

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Published Papers (6 papers)

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Research

19 pages, 14475 KiB  
Article
Human Milk Archaea Associated with Neonatal Gut Colonization and Its Co-Occurrence with Bacteria
by Maricarmen Salas-López, Juan Manuel Vélez-Ixta, Diana Laura Rojas-Guerrero, Alberto Piña-Escobedo, José Manuel Hernández-Hernández, Martín Noé Rangel-Calvillo, Claudia Pérez-Cruz, Karina Corona-Cervantes, Carmen Josefina Juárez-Castelán and Jaime García-Mena
Microorganisms 2025, 13(1), 85; https://doi.org/10.3390/microorganisms13010085 - 4 Jan 2025
Viewed by 977
Abstract
Archaea have been identified as early colonizers of the human intestine, appearing from the first days of life. It is hypothesized that the origin of many of these archaea is through vertical transmission during breastfeeding. In this study, we aimed to characterize the [...] Read more.
Archaea have been identified as early colonizers of the human intestine, appearing from the first days of life. It is hypothesized that the origin of many of these archaea is through vertical transmission during breastfeeding. In this study, we aimed to characterize the archaeal composition in samples of mother-neonate pairs to observe the potential vertical transmission. We performed a cross-sectional study characterizing the archaeal diversity of 40 human colostrum-neonatal stool samples by next-generation sequencing of V5–V6 16S rDNA libraries. Intra- and inter-sample analyses were carried out to describe the Archaeal diversity in each sample type. Human colostrum and neonatal stools presented similar core microbiota, mainly composed of the methanogens Methanoculleus and Methanosarcina. Beta diversity and metabolic prediction results suggest homogeneity between sample types. Further, the co-occurrence network analysis showed associations between Archaea and Bacteria, which might be relevant for these organisms’ presence in the human milk and neonatal stool ecosystems. According to relative abundance proportions, beta diversity, and co-occurrence analyses, the similarities found imply that there is vertical transmission of archaea through breastfeeding. Nonetheless, differential abundances between the sample types suggest other relevant sources for colonizing archaea to the neonatal gut. Full article
(This article belongs to the Special Issue Advances in Diet–Host–Gut Microbiome Interactions)
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14 pages, 2449 KiB  
Article
Investigation of Intestinal Microbes of Five Zokor Species Based on 16S rRNA Sequences
by Yao Zou, Quan Zou, Hui Yang and Chongxuan Han
Microorganisms 2025, 13(1), 27; https://doi.org/10.3390/microorganisms13010027 - 26 Dec 2024
Viewed by 478
Abstract
Zokor is a group of subterranean rodents that are adapted to underground life and feed on plant roots. Here, we investigated the intestinal microbes of five zokor species (Eospalax cansus, Eospalax rothschildi, Eospalax smithi, Myospalax aspalax, and Myospalax [...] Read more.
Zokor is a group of subterranean rodents that are adapted to underground life and feed on plant roots. Here, we investigated the intestinal microbes of five zokor species (Eospalax cansus, Eospalax rothschildi, Eospalax smithi, Myospalax aspalax, and Myospalax psilurus) using 16S amplicon technology combined with bioinformatics. Microbial composition analysis showed similar intestinal microbes but different proportions among five zokor species, and their dominant bacteria corresponded to those of herbivores. To visualize the relationships among samples, PCoA and PERMANOVA tests showed that the intestinal microbes of zokors are largely clustered by host species, but less so by genetics and geographical location. To find microbes that differ among species, LefSe analysis identified Lactobacillus, Muribaculaceae, Lachnospiraceae_NK4A136_group, unclassified_f_Christensenellaceae, and Desulfovibrio as biomarkers for E. cansus, E. rothschildi, E. smithi, M. aspalax, and M. psilurus, respectively. PICRUSt metagenome predictions revealed enriched microbial genes for carbohydrate and amino acid metabolism in E. cansus and E. smithi, and for cofactor and vitamin metabolism as well as glycan biosynthesis and metabolism in E. rothschildi, M. aspalax, and M. psilurus. Our results demonstrated differences in the microbial composition and functions among five zokor species, potentially related to host genetics, and host ecology including dietary habits and habitat environment. These works would provide new insight into understanding how subterranean zokors adapt to their habitats by regulating intestinal microbes. Full article
(This article belongs to the Special Issue Advances in Diet–Host–Gut Microbiome Interactions)
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15 pages, 2718 KiB  
Article
Feeding Expressed Breast Milk Alters the Microbial Network of Breast Milk and Increases Breast Milk Microbiome Diversity over Time
by Melissa A. Woortman, Emily S. Barrett, Thomas G. O’Connor, Steven R. Gill, Kristin Scheible, Jessica Brunner, Haipeng Sun and Maria G. Dominguez-Bello
Microorganisms 2025, 13(1), 12; https://doi.org/10.3390/microorganisms13010012 - 25 Dec 2024
Viewed by 835
Abstract
Breastfeeding supplies nutrition, immunity, and hormonal cues to infants. Feeding expressed breast milk may result in de-phased milk production and feeding times, which distort the real-time circadian cues carried by breast milk. We hypothesized that providing expressed breast milk alters the microbiotas of [...] Read more.
Breastfeeding supplies nutrition, immunity, and hormonal cues to infants. Feeding expressed breast milk may result in de-phased milk production and feeding times, which distort the real-time circadian cues carried by breast milk. We hypothesized that providing expressed breast milk alters the microbiotas of both breast milk and the infant’s gut. To test this hypothesis, we analyzed the microbiota of serial breast milk and infant fecal samples obtained from 14 mother–infant dyads who were lactating, half of which were providing expressed breast milk. Infant fecal microbiota showed lower α-diversity than breast milk microbiota. Bacterial amplicon sequence variant sharing occurred between breast milk and infant feces with no feeding group differences. However, the age-dependent gain in breast milk α-diversity was only significant in the expressed breast milk group and not in the direct breastfeeding group, suggesting that decreased contact with the infant’s mouth influences the milk microbiota. Trending lower connectivity was also noted with breast milk microbes in the direct breastfeeding group, consistent with regular perturbations of the developing baby’s oral microbiota by latching on the breast. The results of this preliminary study urge further research to independently confirm the effects of providing expressed breast milk and their health significance. Full article
(This article belongs to the Special Issue Advances in Diet–Host–Gut Microbiome Interactions)
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24 pages, 4556 KiB  
Article
Mosla Chinensis Extract Enhances Growth Performance, Antioxidant Capacity, and Intestinal Health in Broilers by Modulating Gut Microbiota
by Wei Wang, Yuyu Wang, Peng Huang, Junjuan Zhou, Guifeng Tan, Jianguo Zeng and Wei Liu
Microorganisms 2024, 12(12), 2647; https://doi.org/10.3390/microorganisms12122647 - 20 Dec 2024
Viewed by 636
Abstract
This study aimed to evaluate the effects of Mosla chinensis extract (MCE) on broiler intestinal health. A total of 240 1-day-old Arbor Acres (AA) broilers (balanced for sex) were randomly allocated into four treatment groups, each with six replicates of 10 chickens. The [...] Read more.
This study aimed to evaluate the effects of Mosla chinensis extract (MCE) on broiler intestinal health. A total of 240 1-day-old Arbor Acres (AA) broilers (balanced for sex) were randomly allocated into four treatment groups, each with six replicates of 10 chickens. The study comprised a starter phase (days 1–21) and a grower phase (days 22–42). The control group (C) received a basal diet, while the experimental groups were supplemented with low (S1, 500 mg/kg), medium (S2, 1000 mg/kg), and high doses (S3, 2000 mg/kg) of MCE. The results showed that MCE supplementation significantly improved average daily gain in broilers (p < 0.05) and reduced the feed-to-gain ratio in broilers. Additionally, MCE enhanced the anti-inflammatory and antioxidant capacity of broilers. In the duodenum and cecum, MCE significantly upregulated the expression of tight junction proteins Claudin-1, and Occludin, with the high-dose group showing the strongest effect on intestinal barrier protection (p < 0.05). There was no significant difference in ZO-1 in dudenum (p > 0.05). Microbial analysis indicated that MCE supplementation significantly reduced the Chao and Sobs indices in both the small and large intestines (p < 0.05). At the same time, the Coverage index of the small intestine increased, with the high-dose group demonstrating the most pronounced effect. Beta diversity analysis revealed that MCE had a significant modulatory effect on the microbial composition in the large intestine (p < 0.05), with a comparatively smaller impact on the small intestine. Furthermore, MCE supplementation significantly increased the relative abundance of Ruminococcaceae and Alistipes in the large intestine, along with beneficial genera that promote short-chain fatty acid (SCFA) production, thus optimizing the gut microecological environment. Correlation analysis of SCFAs further confirmed a significant association between the enriched microbiota and the production of acetate, propionate, and butyrate (p < 0.05). In conclusion, dietary supplementation with MCE promotes healthy growth and feed intake in broilers and exhibits anti-inflammatory and antioxidant effects. By optimizing gut microbiota composition, enhancing intestinal barrier function, and promoting SCFA production, MCE effectively maintains gut microecological balance, supporting broiler intestinal health. Full article
(This article belongs to the Special Issue Advances in Diet–Host–Gut Microbiome Interactions)
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18 pages, 3554 KiB  
Article
Wild-Mouse-Derived Gut Microbiome Transplantation in Laboratory Mice Partly Alleviates House-Dust-Mite-Induced Allergic Airway Inflammation
by Md Zohorul Islam, Danica Jozipovic, Pablo Atienza Lopez, Lukasz Krych, Banny Silva Barbosa Correia, Hanne Christine Bertram, Axel Kornerup Hansen and Camilla Hartmann Friis Hansen
Microorganisms 2024, 12(12), 2499; https://doi.org/10.3390/microorganisms12122499 - 4 Dec 2024
Viewed by 1148
Abstract
Laboratory mice are instrumental for preclinical research but there are serious concerns that the use of a clean standardized environment for specific-pathogen-free (SPF) mice results in poor bench-to-bedside translation due to their immature immune system. The aim of the present study was to [...] Read more.
Laboratory mice are instrumental for preclinical research but there are serious concerns that the use of a clean standardized environment for specific-pathogen-free (SPF) mice results in poor bench-to-bedside translation due to their immature immune system. The aim of the present study was to test the importance of the gut microbiota in wild vs. SPF mice for evaluating host immune responses in a house-dust-mite-induced allergic airway inflammation model without the influence of pathogens. The wild mouse microbiome reduced histopathological changes and TNF-α in the lungs and serum when transplanted to microbiota-depleted mice compared to mice transplanted with the microbiome from SPF mice. Moreover, the colonic gene expression of Gata3 was significantly lower in the wild microbiome-associated mice, whereas Muc1 was more highly expressed in both the ileum and colon. Intestinal microbiome and metabolomic analyses revealed distinct profiles associated with the wild-derived microbiome. The wild-mouse microbiome thus partly reduced sensitivity to house-dust-mite-induced allergic airway inflammation compared to the SPF mouse microbiome, and preclinical studies using this model should consider using both ‘dirty’ rewilded and SPF mice for testing new therapeutic compounds due to the significant effects of their respective microbiomes and derived metabolites on host immune responses. Full article
(This article belongs to the Special Issue Advances in Diet–Host–Gut Microbiome Interactions)
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14 pages, 590 KiB  
Article
Parameter Estimation of Host Genomic and Gut Microbiota Contribution to Growth and Feed Efficiency Traits in Meat Rabbits
by Xinyang Tian, Junkun Zhou, Yinghe Qin, Kai Zhang, Wenqiang Sun, Song-Jia Lai, Xianbo Jia and Shi-Yi Chen
Microorganisms 2024, 12(10), 2091; https://doi.org/10.3390/microorganisms12102091 - 19 Oct 2024
Viewed by 954
Abstract
Rabbits can efficiently utilize plant fibers that are indigestible to humans, and hence may contribute to the alleviation of feed–food competition. Therefore, it is economically and ecologically important to genetically improve the growth performance and feed efficiency of meat rabbits. In this study, [...] Read more.
Rabbits can efficiently utilize plant fibers that are indigestible to humans, and hence may contribute to the alleviation of feed–food competition. Therefore, it is economically and ecologically important to genetically improve the growth performance and feed efficiency of meat rabbits. In this study, we combined pedigree, genomic, and gut microbiota data to estimate genetic and microbial parameters for nine growth and feed efficiency traits of 739 New Zealand White rabbits, including body weight (BW) at 35 (BW35), 70 (BW70), and 84 (BW84) days of age, and average daily gain (ADG), feed conversion ratio (FCR), and residual feed intake (RFI) within two age intervals of 35–70 days (ADG70, FCR70, and RFI70) and 35–84 days (ADG84, FCR84, and RFI84). Based on single-step genomic best linear unbiased prediction, three BW traits and two ADG traits had the high estimates (±standard error, SE) of heritability, ranging from 0.44 ± 0.13 of BW35 to 0.66 ± 0.08 of BW70. Moderate heritabilities were observed for RFI70 (0.22 ± 0.07) and RFI84 (0.29 ± 0.07), whereas the estimates did not significantly deviate from zero for the two FCR traits. There was moderate positive genetic correlation (±SE) between BW70 and ADG70 (0.579 ± 0.086), but BW70 did not correlate with RFI70. Based on microbial best linear unbiased prediction, the estimates of microbiability did not significantly deviate from zero for any trait. Based on the combined use of genomic and gut microbiota data, the parameters obtained in this study could help us to implement efficient breeding schemes in meat rabbits. Full article
(This article belongs to the Special Issue Advances in Diet–Host–Gut Microbiome Interactions)
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