The Core Equine Faecal Microbiome: A Broader Perspective

Background: Equine gut microbiology studies to date have primarily focused on horses and ponies which represent only one of the 8 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 fibre. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fibre degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden current bacterial, anaerobic fungal and archaeal knowledge of the equine hindgut to multiple species of equines. Taxa core to all the equine faecal samples (n=70) were determined and observations of the effect of equine type (horse, donkey, horse × donkey and zebras) on the hindgut microbiota conducted. Results: Equine type influenced both microbial concentrations and community composition. Donkeys generally were most distinct from the other equine types, with horses and zebra not differing. Despite this, a common bacterial core of 8 OTU and 16 genus level groupings of OTU was found in all the equines studied. This bacterial core represented a much larger proportion of the equine faecal microbiota than previously reported, primarily due to the detection of dominant core taxa belonging to the Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaete phyla. The majority of the core bacterial taxa lacked 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 dominant.Conclusions: Whilst differences were observed between equine types, a core faecal microbiome existed across all the equines. This core was composed primarily of a few dominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the dominant bacterial as well as anaerobic fungal taxa in the equine hindgut is of concern, and highlights an urgent need to isolate these taxa. Only then can fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem be elucidated.