Domesticated equine species and their derived hybrids differ in their fecal microbiota

Abstract

Background: Compared to horses and ponies, donkeys have increased degradation of dietary fiber. The longer total mean retention time of feed in the donkey gut has been proposed to be the basis of this, because of the increased time available for feed to be acted upon by enzymes and the gut microbiota. However, differences in terms of microbial concentrations and/or community composition in the hindgut may also underpin the increased degradation of fiber in donkeys. Therefore, a study was conducted to assess if differences existed between the fecal microbiota of pony, donkey and hybrids derived from them (i.e. pony × donkey) when fed the same forage diet. Results: Fecal community composition of prokaryotes and anaerobic fungi significantly differed between equine types. The relative abundance of two bacterial genera was significantly higher in donkey compared to both pony and pony x donkey: Lachnoclostridium 10 and 'probable genus 10' from the Lachnospiraceae family. The relative abundance of Piromyces was significantly lower in donkey compared to pony × donkey, with pony not significantly differing from either of the other equine types. In contrast, the uncultivated genus SK3 was only found in donkey (4 of the 8 animals). The number of anaerobic fungal OTUs was also significantly higher in donkey than in the other two equine types, with no significant differences found between pony and pony × donkey. Equine types did not significantly differ with respect to prokaryotic alpha diversity, fecal dry matter content or fecal concentrations of bacteria, archaea and anaerobic fungi. Conclusions: Donkey fecal microbiota differed from that of both pony and pony × donkey. These differences related to a higher relative abundance and diversity of taxa with known, or speculated, roles in plant material degradation. These findings are consistent with the previously reported increased fiber degradation in donkeys compared to ponies, and suggest that the hindgut microbiota plays a role. This offers novel opportunities for pony and pony × donkey to extract more energy from dietary fiber via microbial mediated strategies. This could potentially decrease the need for energy dense feeds which are a risk factor for gut-mediated disease.

Comparison of In Vivo and In Vitro Digestibility in Donkeys

“…Most of the bacterial taxa of this core lack cultured representation; their availability is essential to gain fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem and that of the donkey in particular. In another trial, Edwards et al [ 8 ] found that donkey fecal microbiota differed from that of both pony and pony × donkey, and these differences were related to a higher abundance and diversity of taxa with known (or speculated) roles in fiber degradation. The findings of these trials suggest that the specific composition of hindgut microbiota of donkeys plays an essential role in fiber digestion.…”

“…Their large intestine leads to a higher digestibility of organic matter, gross energy and fiber fractions than in horses or ponies [ 4 , 5 , 6 ]. According to Edwards et al [ 7 , 8 ], donkeys have a fecal microbiota concentration and a community composition that differ from those of other equine types, and this diversity plays an essential role in fiber digestion. Liu et al [ 9 ] studied the microbiota at different sites of the gastrointestinal tract of donkeys, finding a higher microbial concentration in the hindgut than in the foregut.…”

Anaerobic Fungi: Past, Present, and Future

“…Anaerobic fungi were reported to be present in domesticated and non-domesticated equine species, with the AF community composition in horses and ponies being more similar to zebras than donkeys (Edwards et al, 2020b). In a separate study, AF diversity in donkeys was shown to be higher when compared to that of ponies and pony × donkey hybrids (Edwards et al, 2020a). Several studies have revealed that the genus Khoyollomyces (formerly known as AL1) is almost exclusively found in equines (Liggenstoffer et al, 2010;Mura et al, 2019;Edwards et al, 2020b;Hanafy et al, 2020).…”

Advances In The Understanding of The Commensal Eukaryota And Viruses Of The Herbivore Gut

“…Anaerobic fungi were reported to be present in domesticated and non-domesticated equine species, with the AF community composition in horses and ponies being more similar to zebras than donkeys (Edwards et al, 2020b). In a separate study, AF diversity in donkeys was shown to be higher when compared to that of ponies and pony × donkey hybrids (Edwards et al, 2020a). Several studies have revealed that the genus Khoyollomyces (formerly known as AL1) is almost exclusively found in equines Mura et al, 2019;Edwards et al, 2020b;Hanafy et al, 2020).…”