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Differential shaping of equine gut microbiota structure and function by breed and feeding regimen.
Abstract: The gut microbiota plays an essential role in host energy metabolism and immune function. Horses are non-ruminant herbivores that rely heavily on hindgut microbial fermentation to meet their energy requirements. However, the relative contributions of host genetic background (breed) and environmental factors (feeding regimen and geographical location) to shaping the equine gut microbiota remain poorly understood. Unassigned: In this study, 16S rRNA gene sequencing and functional prediction analysis were performed on 139 equine fecal samples to systematically investigate the differential effects of breed and feeding regimen on the gut microbiota. Samples were collected from 30 Thoroughbreds (TH), 31 stabled hybrid horses (HH1), 30 grazing hybrid horses (HH2) (with HH1 and HH2 sired by Thoroughbreds out of Mongolian mares), 32 Mongolian horses (MH), and 16 Warmblood horses (WBH1 and WBH2). Alpha and beta diversity analyses, taxonomic profiling, and PERMANOVA were used to assess microbial composition and the contributions of different factors. Unassigned: Alpha diversity analysis revealed that the richness and diversity of the TH, HH1, HH2, and MH groups were significantly higher than those of the Warmblood horses ( < 0.001), with Mongolian horses exhibiting the highest diversity and the hybrids showing intermediate levels between their parental breeds. Regarding taxonomic composition, the TH, HH1, HH2, and MH groups shared a microbial structure dominated by Firmicutes and Bacteroidota, yet each possessed distinct characteristics: Thoroughbreds were enriched with Treponema; Mongolian horses harbored the highest abundances of Rikenellaceae_RC9_gut_group and NK4A214_group; and the grazing hybrid horses developed a fiber-degrading bacterial community centered on and , demonstrating breed-specific microbial features. In contrast, the Warmblood horses exhibited a gut microbiota with distinct features characterized by significantly reduced microbial diversity and core fiber-degrading genera, concomitant with an enrichment of environmental-associated bacteria from the phylum Proteobacteria (e.g., , ) and other genera (e.g., , ). PERMANOVA analysis further quantified the contributions of different factors: breed explained 44.8% of the total variation (R² = 0.448, p < 0.001), followed by feeding regimen (10.3%, p < 0.001) and geographical location (2.7%, *p* < 0.01), confirming breed as the predominant factor. Unassigned: This study provides evidence that breed establishes the foundational framework of the gut microbiota, while feeding regimen performs fine-tuning functions. We also systematically characterized the unique microbial composition of Warmblood horses, offering a scientific basis for breed-specific health management, precision nutritional interventions, and future disease risk monitoring in horses. Although all horses appeared clinically healthy, the distinct microbial composition observed in Warmblood horses warrants further investigation to determine its biological significance.
Copyright © 2026 Lin, Qiri, Du, Dugarjaviin, Cao, Fang, Yun, Li, Gong, Ding, Bou, Su, Chen, Xing, Bai and Zhao.
Publication Date: 2026-07-16 PubMed ID: 42549200PubMed Central: PMC13430720DOI: 10.3389/fmicb.2026.1852554Google Scholar: Lookup The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Journal Article
Summary
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Research Summary
- This study investigates how horse breed and feeding practices influence the structure and function of the gut microbiota in horses.
- Through analysis of fecal samples from various breeds and feeding regimens, the study highlights breed as the primary factor shaping gut microbial composition, with feeding regimen having a secondary, modifying role.
Introduction to Equine Gut Microbiota
- The gut microbiota refers to the community of microorganisms residing in the digestive tract, crucial for energy metabolism and immune responses in the host.
- Horses are non-ruminant herbivores relying predominantly on microbial fermentation in the hindgut to digest fiber and generate energy.
- Understanding how genetics (breed) and environment (diet and geography) affect this microbiota can reveal insights into equine health and nutrition.
Study Design and Methods
- Collected fecal samples from 139 horses representing five groups: Thoroughbreds (TH), stabled hybrid horses (HH1), grazing hybrid horses (HH2), Mongolian horses (MH), and Warmblood horses (WBH1 and WBH2).
- Hybrid horses (HH1 and HH2) were offspring of Thoroughbred stallions and Mongolian mares, allowing observation of intermediate microbial traits.
- Applied 16S rRNA gene sequencing to characterize bacterial communities in the samples.
- Conducted alpha diversity (within-sample diversity) and beta diversity (between-sample differences) analyses, taxonomic profiling, and PERMANOVA for multivariate statistical testing.
- Performed functional prediction analysis to infer microbial community functions based on gene sequencing data.
Key Findings on Microbial Diversity
- Alpha diversity was significantly higher in Thoroughbreds, hybrid horses (both stabled and grazing), and Mongolian horses compared to Warmbloods (p < 0.001).
- Mongolian horses exhibited the highest microbial richness and diversity overall.
- Hybrid horses showed microbial diversity levels intermediate between Thoroughbreds and Mongolian horses, reflecting their mixed genetic backgrounds.
- Warmblood horses displayed reduced microbial diversity, a notable deviation among studied breeds.
Taxonomic Composition of Gut Microbiota
- Across TH, HH1, HH2, and MH breeds, Firmicutes and Bacteroidota phyla dominated the microbial community, crucial for fiber fermentation and energy extraction.
- Distinct microbial signatures by breed included:
- Thoroughbreds enriched with Treponema, a genus linked to carbohydrate metabolism.
- Mongolian horses abundant in Rikenellaceae_RC9_gut_group and NK4A214_group, which are associated with efficient fiber degradation.
- Grazing hybrid horses exhibited fiber-degrading bacteria focused on specific genera (names missing in abstract, likely key cellulolytic bacteria).
- Warmblood horses’ microbiota were characterized by:
- Significantly reduced diversity and fewer core fiber-degrading bacteria, indicating altered gut fermentation capacity.
- Increased presence of environmental bacteria belonging to the phylum Proteobacteria (such as unnamed genera), which might reflect environmental exposure or dysbiosis.
- Enrichment of other genera not typically dominant in healthy equine gut microbiota, suggesting distinctive, possibly less beneficial microbial profiles.
Statistical Analysis of Influencing Factors
- PERMANOVA analysis quantified the relative influence of host and environmental factors on gut microbiota variation:
- Breed accounted for 44.8% of total microbial variation (highly significant, p < 0.001), establishing it as the primary shaping force.
- Feeding regimen explained 10.3% of variation (p < 0.001), confirming diet’s role in fine-tuning the microbial community.
- Geographical location had a smaller but significant effect (2.7%, p < 0.01).
Implications and Conclusions
- Breed provides a foundational framework determining equine gut microbiota composition, potentially driven by host genetics and physiology.
- Feeding regimen modulates this framework, influencing microbial functions related to digestion and health.
- Warmblood horses uniquely exhibit lower microbial diversity and enrichment of environmental bacteria, which might have implications for their digestive health or disease susceptibility.
- These findings support the idea of breed-specific health management and tailored nutritional strategies to maintain optimal gut health.
- The study emphasizes the need for further research into the biological significance of the distinct microbiota observed in Warmbloods, even though all horses analyzed were clinically healthy.
Cite This Article
APA
Lin Y, Qiri G, Du M, Dugarjaviin M, Cao J, Fang X, Yun S, Li X, Gong W, Ding W, Bou T, Su S, Chen J, Xing N, Bai D, Zhao Y.
(2026).
Differential shaping of equine gut microbiota structure and function by breed and feeding regimen.
Front Microbiol, 17, 1852554.
https://doi.org/10.3389/fmicb.2026.1852554 Publication
Researcher Affiliations
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Xing An Polytechnic University, Ulanhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
Conflict of Interest Statement
The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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