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Frontiers in microbiology2026; 17; 1807081; doi: 10.3389/fmicb.2026.1807081

Comparative metagenomic analysis of gut microbiomes in Yunnan ponies and Dutch warmblood horses.

Abstract: The Yunnan pony is an officially protected pony breed in China. However, its gut microbiome characteristics remain largely unexplored. This study aimed to compare the gut microbiome and antibiotic resistance genes (ARGs) profiles between Yunnan ponies and Dutch warmblood horses. Unassigned: A total of 14 fresh fecal samples were collected from Yunnan ponies and Dutch warmblood horses. Metagenomic sequencing was employed to comprehensively analyze and compare the gut microbial composition, function, and ARGs profiles between the two breeds. Unassigned: The results showed no significant differences between the two breeds in core phylum composition or overall microbial diversity. A total of 146 bacterial genera were identified with significant differences at the genus level. Functional analysis revealed that the gut microbiota of Yunnan ponies was significantly enriched in pathways related to carbohydrate metabolism and pectin degradation, which are involved in basic energy acquisition. In contrast, Dutch warmblood horses were more enriched in host immune interaction pathways such as Toll-like receptor signaling. Analysis of ARGs indicated that while there was no difference in the overall diversity of ARGs between the two groups. Their association networks with specific bacterial hosts were markedly distinct, and the dominant ARG subtypes differed. Unassigned: This study provides a descriptive characterization of the gut microbiome of Yunnan ponies, offering baseline data for future research on the conservation of this genetic resource and its health management in breeding.
Publication Date: 2026-06-05 PubMed ID: 42326408PubMed Central: PMC13279432DOI: 10.3389/fmicb.2026.1807081Google Scholar: Lookup
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  • Journal Article

Summary

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Overview

  • This study compared the gut microbiomes and antibiotic resistance gene (ARG) profiles of Yunnan ponies, a protected Chinese breed, and Dutch warmblood horses using metagenomic sequencing.
  • Researchers aimed to understand differences in microbial composition, function, and ARG presence to inform conservation and health management efforts.

Research Background

  • The Yunnan pony is a recognized and protected breed in China with little known about its gut microbial community.
  • The gut microbiome plays a crucial role in animal health, digestion, immunity, and resistance to pathogens.
  • Comparing the microbiomes of different horse breeds helps identify unique features and potential adaptations related to diet or environment.

Methodology

  • Sample Collection:
    • Collected 14 fresh fecal samples total from two horse groups: Yunnan ponies and Dutch warmblood horses.
  • Metagenomic Sequencing:
    • Performed high-throughput sequencing to comprehensively profile microbial taxa and functions within the gut samples.
    • Focused on identifying both the microbial composition (which bacteria are present) and antibiotic resistance genes (ARGs).

Key Findings: Microbial Composition

  • Core Phyla:
    • No significant differences in the overall core phylum-level composition between the Yunnan ponies and Dutch warmblood horses.
  • Diversity:
    • Microbial diversity (richness and evenness of species) was broadly similar in both breeds.
  • Genus-Level Differences:
    • Despite similar phylum-level patterns, 146 bacterial genera showed significant abundance differences between the breeds.

Functional Analysis of Gut Microbiota

  • Yunnan Ponies:
    • Gut microbiota enriched for pathways involved in carbohydrate metabolism, including pectin degradation.
    • Indicates a microbiome specialized in breaking down plant fibers for energy acquisition, likely reflecting adaptation to their diet or environment.
  • Dutch Warmblood Horses:
    • Gut microbiota showed enrichment in host immune interaction pathways, such as Toll-like receptor signaling.
    • Suggests a greater microbial influence on modulating or interacting with host immune responses.

Antibiotic Resistance Gene (ARG) Profiles

  • Overall ARG Diversity:
    • No significant difference in overall ARG diversity between Yunnan ponies and Dutch warmblood horses.
  • ARG-Bacteria Associations:
    • Networks linking specific ARGs to their bacterial hosts differed markedly between the two breeds.
  • Dominant ARG Subtypes:
    • The most common types of ARGs varied, indicating differences in potential antibiotic resistance mechanisms prevalent in each breed’s microbiome.

Significance and Implications

  • This study offers the first detailed characterization of the gut microbiome in the Yunnan pony, filling a knowledge gap for this protected breed.
  • Baseline gut microbiome data can inform conservation strategies efforts by revealing dietary adaptations and microbial health indicators.
  • Understanding breed-specific microbiome functions and ARG profiles can assist in managing health and antibiotic resistance risks in breeding programs.
  • Findings highlight how different breeds harbor unique gut microbial ecosystems despite broad similarities, reflecting genetic, dietary, and environmental influences.

Cite This Article

APA
Cha J, Yang J, Zhang Z, Qian L, Yang F, Li S, Li J, Jian Z, Cheng W. (2026). Comparative metagenomic analysis of gut microbiomes in Yunnan ponies and Dutch warmblood horses. Front Microbiol, 17, 1807081. https://doi.org/10.3389/fmicb.2026.1807081

Publication

ISSN: 1664-302X
NlmUniqueID: 101548977
Country: Switzerland
Language: English
Volume: 17
Pages: 1807081
PII: 1807081

Researcher Affiliations

Cha, Jinlong
  • Yunnan Vocational College of Agriculture, Kunming, China.
  • College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China.
Yang, Jieyan
  • College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China.
Zhang, Zifang
  • Yunnan Vocational College of Agriculture, Kunming, China.
Qian, Lindong
  • Yunnan Vocational College of Agriculture, Kunming, China.
Yang, Fangxiao
  • Yunnan Vocational College of Agriculture, Kunming, China.
Li, Shiyou
  • Yunnan Vocational College of Agriculture, Kunming, China.
Li, Ju
  • Yunnan Vocational College of Agriculture, Kunming, China.
Jian, Zonghui
  • Yunnan Vocational College of Agriculture, Kunming, China.
Cheng, Wenjie
  • College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China.
  • First People's Hospital of Kunming City, Kunming, 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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