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


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).


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.


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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Research output

Equidae hindgut anaerobic fungi: a key unexplored taxa of central importance to dietary fibre degradation

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Faecal sampling and analysis to survey ecology of anaerobic fungi. DNA extraction and PCR. Use of in vitro equine hindgut model where necessary.


1) Which anaerobic fungi are present in equids? It is hypothesised that equid specific anaerobic fungal taxa exist. 2) Do anaerobic fungi differ in ponies, donkeys and mules? It is hypothesised that the community composition of anaerobic fungi is not affected by host genotype but their quantity is (donkeys>mules>ponies). 3) Are equine anaerobic fungi different from those found in ruminants? It is hypothesised that equid specific anaerobic fungal taxa have genetic, metabolic and physiological properties that are distinct from those that have been previously described for ruminal anaerobic fungi. 4) What is the impact of anaerobic fungi on forage fermentation in the equine hindgut? It is hypothesised that anaerobic fungi improve the degradation of forage in the equine hindgut, and enhance the number and associated activity of bacteria, archaea and protozoa.

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