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

J E Edwards,F Burden,W F Pellikaan,S A Shetty,J Dijkstra,P Van Den Berg,D A Van Doorn,D A Van Doorn,H Smidt

doi:10.1186/s42523-020-0023-1

Abstract

BackgroundEquine 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).ResultsEquine 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.ConclusionsWhilst 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.

Highlights

Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species
Microbial concentrations Due to equine type being associated with differences in fecal dry matter content (P = 0.006; Additional file 2: Figure S1), where zebra fecal dry matter was significantly higher than that of horse and of donkey, microbial concentration data were analyzed on a dry weight basis
Equine type was associated with differences in fecal bacterial concentrations (P = 0.016), with horse and zebra both being significantly lower than horse × donkey, and donkey being intermediate (Fig. 1a)

Summary

Introduction

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. There has been a move to characterizing the equine hindgut microbiota using high throughput sequencing of fecal [1,2,3,4,5,6,7] and digesta samples [8, 9], as well as determining the equine fecal and hindgut core composition [3, 7, 8, 10, 11]. Studies of the bacterial core to date have focused only on domesticated horses and/or ponies, which represent only one of the eight extant species of the equid family [15]

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Discussion

Conclusion