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Animal microbiome2020; 2(1); 6; doi: 10.1186/s42523-020-0023-1

Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species.

Abstract: Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species. This is despite asses and mules comprising almost half of the world's domesticated equines, and donkeys being superior to horses/ponies in their ability to degrade dietary fiber. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fiber degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden the current knowledge of bacterial, anaerobic fungal and archaeal diversity of the equine fecal microbiota to multiple species of equines. Core taxa shared by all the equine fecal samples (n = 70) were determined and an overview given of the microbiota across different equine types (horse, donkey, horse × donkey and zebra). Results: Equine type was associated with differences in both fecal microbial concentrations and community composition. Donkey was generally most distinct from the other equine types, with horse and zebra not differing. Despite this, a common bacterial core of eight OTUs (out of 2070) and 16 genus level groupings (out of 231) was found in all the fecal samples. This bacterial core represented a much larger proportion of the equine fecal microbiota than previously reported, primarily due to the detection of predominant core taxa belonging to the phyla Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaetes. The majority of the core bacterial taxa lack cultured representation. Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either despite several taxa being prevalent and predominant. Conclusions: Whilst differences were observed between equine types, a core fecal microbiota existed across all the equines. This core was composed primarily of a few predominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the predominant taxa needs to be addressed, as their availability is essential to gain fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem.
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Publication Date: 2020-02-12 PubMed ID: 33499982PubMed Central: PMC7807809DOI: 10.1186/s42523-020-0023-1Google Scholar: Lookup
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  • Journal Article

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.

The research examines the diversity in the gut bacteria, fungi, and archaea present in different equine (horse family) species – including horses, donkeys, zebras, and horse-donkey hybrids. The study finds that despite some differences in microbial community composition, there exists a common core of microbes shared across all equine species.

Study Objectives and Approach

  • The primary aim of the study was to broaden our understanding of equine gut microbiota, focusing not just on horses and ponies, but across diverse (sub)species such as donkeys, zebras, and horse-donkey hybrids.
  • The study explored both bacterial and non-bacterial organisms, including anaerobic fungi and methanogenic archaea, both of which are important for the degradation of dietary fiber.
  • Scientists used fecal samples from these animals to determine the core taxa (major groups of species) shared by all equine types.

Key Findings

  • The fecal microbial concentrations and community compositions differed among the horse, donkey, zebra, and horse-donkey hybrids. Donkeys were found to have the most distinctive gut microbiota, while horses and zebras showed no notable differences.
  • Despite these variations, a common core of eight OTUs (operational taxonomic units – a way to classify groups of closely related individuals) and 16 genus-level groups was found in all the fecal samples.
  • This core constitutes a much larger proportion of the equine gut microbiota than was previously known. The core taxa are predominantly bacteria belonging to the Kiritimatiellaeota and Spirochaetes phyla.
  • Archaea and anaerobic fungi were found in all animals, but no core taxon was detected for them, despite their presence in many samples.

Implications and Conclusions

  • While the study observed differences between equine types, it identified a substantial core microbiota across all equines studied. This common core is mainly a few predominant bacterial taxa.
  • Most of these bacterial taxa have not been cultured in the lab, highlighting a gap in our understanding of their function. Resolving this gap would provide invaluable insights into the microbial functions that underpin the equine gut ecosystem.

Cite This Article

APA
Edwards JE, Shetty SA, van den Berg P, Burden F, van Doorn DA, Pellikaan WF, Dijkstra J, Smidt H. (2020). Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species. Anim Microbiome, 2(1), 6. https://doi.org/10.1186/s42523-020-0023-1

Publication

Animal microbiome
ISSN: 2524-4671
NlmUniqueID: 101759457
Country: England
Language: English
Volume: 2
Issue: 1
Pages: 6
PII: 6

Researcher Affiliations

Edwards, J E
  • Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE, Netherlands. joanee2002@hotmail.com.
Shetty, S A
  • Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE, Netherlands.
van den Berg, P
  • Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE, Netherlands.
Burden, F
  • The Donkey Sanctuary, Sidmouth, Devon, EX10 ONU, UK.
van Doorn, D A
  • Division of Nutrition, Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CM, Netherlands.
  • Department of Equine Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, Netherlands.
Pellikaan, W F
  • Animal Nutrition Group, Wageningen University & Research, Wageningen, 6708 WD, Netherlands.
Dijkstra, J
  • Animal Nutrition Group, Wageningen University & Research, Wageningen, 6708 WD, Netherlands.
Smidt, H
  • Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE, Netherlands. hauke.smidt@wur.nl.

Grant Funding

  • 706899 / H2020 Marie Sku0142odowska-Curie Actions

Conflict of Interest Statement

The authors declare that they have no competing interests.

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