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Microbiome2023; 11(1); 7; doi: 10.1186/s40168-022-01448-z

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse.

Abstract: As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses. Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing the wide use of antibiotics in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in racehorses than in nonracehorses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fibre fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance. Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalogue for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome. Video Abstract.
© 2023. The Author(s).
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Publication Date: 2023-01-12 PubMed ID: 36631912PubMed Central: PMC9835274DOI: 10.1186/s40168-022-01448-zGoogle Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This study investigates the gut microbiota of horses and its impact on their health and performance. The researchers sequenced the gut microbiomes from 242 horses and identified over 4,000 new species. They observed high diversity of antibiotic resistance genes and a correlation between certain microbes and enhanced athletic performance in racehorses.

Objective

  • The study aimed to understand the structure and function of the horse gut microbiome by assembling microbial metagenome-assembled genomes (MAGs). Understanding the horse gut microbiota could give insights into the health, disease resilience, and performance-related characteristics of horses.

Methodology

  • The researchers used approximately 2.2 terabytes of metagenomic sequencing data from samples taken from the guts of 242 horses. These included 110 samples from the caecum and 132 samples from the rectum (faeces).
  • Their analysis yielded 4142 microbial MAGs, of which over 96% represented new species, based on their analysis. Among these, they were able to assemble 13 circular whole-chromosome bacterial genomes representing novel species from long-read data.

Findings

  • The assembled MAGs contained more than 313,568 predicted carbohydrate-active enzymes (CAZy), over half of which had low similarity matches in public CAZy databases. This suggests a vast diversity of functional potential in the horse gut microbiome.
  • The researchers also identified a high abundance and diversity of antibiotic resistance genes (ARG), reflecting widespread use of antibiotics in horse management.
  • At least 36 of the MAGs (belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were more abundant in racehorses than in nonracehorses. These MAGs contained every gene in a major pathway for producing acetate and butyrate by fibre fermentation, suggesting that they could provide a greater amount of short-chain fatty acids available to fuel athletic performance.

Conclusion

  • The study has generated an extensive microbial genome catalogue for the horse gut microbiome. This dataset forms a valuable resource for further research into performance-enhancing microbes, horse health and the gut microbiome more broadly.

Cite This Article

APA
Li C, Li X, Guo R, Ni W, Liu K, Liu Z, Dai J, Xu Y, Abduriyim S, Wu Z, Zeng Y, Lei B, Zhang Y, Wang Y, Zeng W, Zhang Q, Chen C, Qiao J, Liu C, Hu S. (2023). Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse. Microbiome, 11(1), 7. https://doi.org/10.1186/s40168-022-01448-z

Publication

Microbiome
ISSN: 2049-2618
NlmUniqueID: 101615147
Country: England
Language: English
Volume: 11
Issue: 1
Pages: 7
PII: 7

Researcher Affiliations

Li, Cunyuan
  • College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
  • Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003, Xinjiang, China.
  • College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang, China.
Li, Xiaoyue
  • College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
  • Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003, Xinjiang, China.
Guo, Rongjun
  • Novogene Bioinformatics Institute, Beijing, 100000, China.
Ni, Wei
  • College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China. niweiwonderful@sina.com.
  • Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003, Xinjiang, China. niweiwonderful@sina.com.
Liu, Kaiping
  • College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
  • State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 830003, Xinjiang, China.
Liu, Zhuang
  • College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
Dai, Jihong
  • College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
Xu, Yueren
  • College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
Abduriyim, Shamshidin
  • College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
Wu, Zhuangyuan
  • Xinjiang Altay Animal Husbandry and Veterinary Station, Altay, 836501, Xinjiang, China.
Zeng, Yaqi
  • College of Animal Science, Xinjiang Agricultural University, Urumqi, 830000, Xinjiang, China.
Lei, Bingbing
  • College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
Zhang, Yunfeng
  • State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 830003, Xinjiang, China.
Wang, Yue
  • College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
Zeng, Weibin
  • College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang, China.
Zhang, Qiang
  • College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang, China.
Chen, Chuangfu
  • College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang, China.
Qiao, Jun
  • College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang, China.
Liu, Chen
  • Novogene Bioinformatics Institute, Beijing, 100000, China. liuchen@novogene.com.
Hu, Shengwei
  • College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China. hushengwei@163.com.
  • Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003, Xinjiang, China. hushengwei@163.com.

MeSH Terms

  • Horses / genetics
  • Humans
  • Animals
  • Metagenome
  • Genome, Bacterial
  • Gastrointestinal Microbiome / genetics
  • Drug Resistance, Microbial
  • Athletic Performance
  • Metagenomics

Conflict of Interest Statement

The authors declare that they have no competing interests.

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