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

Abstract

Background: 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.

Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters

“…Spirochaetaceae and Kiritimatiellae are also present at modest relative abundances; however, their metabolic niches are currently less well characterized. These results are consistent with findings from domestic, feral, and wild horse systems (Antwis et al, 2018;Costa et al, 2015;Metcalf et al, 2017) and a comprehensive comparison of wild and domestic equid species (Edwards et al, 2020). Unlike previous studies, however, we detected no effect of age, probably because we constrained sampling to horses of at least 3 years of age, and the horse microbiome appears to reach maturation after ~1 year (Antwis et al, 2018;De La Torre et al, 2019;Metcalf et al, 2017).…”

Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas

“…Finally, drier periods were also characterized by a large increase in the RFP12 family (i.e., ~ 30% versus ~ 18% in wetter periods) from the Kiritimatiellaeota phylum. The RFP12 family remains poorly characterized but is increasingly recognized as being a keystone bacterial group in the hindgut of horses ( Equus ferus caballus ) [ 70 – 72 ], and a common inhabitant of the rumen of sheep ( Ovis aries ) or cattle [ 73 – 75 ]. The bacterial sequences belonging to the RFP12 family found in the gelada feces were, on average, 97% similar to bacterial sequences found in the feces of various hindgut herbivorous fermenters [ 48 ] and, to a lesser extent, in the rumen of foregut fermenters (Table S 3 ).…”

Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas

“…~30% versus ~18% in wetter periods) from the Kiritimatiellaeota phylum. The RFP12 family remains poorly characterized but is increasingly recognized as being a keystone bacterial group in the hindgut of horses (Steelman et al 2012;Costa et al 2015;Edwards et al 2020), and a common inhabitant of the rumen of sheep or cattle (Wang et al 2017;De Mulder et al 2017;Ribeiro et al 2017). This suggests that it might be a keystone bacterial group for the digestion of some underground food components commonly eaten by the geladas during dry periods.…”