Donkeys have the most distinct microbial composition in their faeces among the equine species, according to researchers, while no differences were seen between horses and zebras.
Joan Edwards and her colleagues, writing in the journal Animal Microbiome, noted that equine gut microbiology studies to date had mostly focused on horses and ponies, which represent just one of the eight 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.”
They also noted that little attention had been given to potentially useful anaerobic fungi and archaea, even though anaerobic fungi are potent fiber-degrading organisms, the activity of which is enhanced by methane-producing archaea.
The researchers from Wageningen and Utrecht universities in the Netherlands set out to broaden the current knowledge of bacterial, anaerobic fungal and archaeal diversity in the equine fecal microbiota.
The hindgut microbiome is key to the ability of equines to degrade dietary fiber, as equines themselves lack fiber-degrading enzymes.
The study team used molecular testing to identify the microbes present in 70 healthy equines, aged 4 to 16, comprising 18 horses and ponies, 18 donkeys, 18 donkey-horse hybrids, with the rest made up of several different (sub) species of zebras.
The researchers found that equine type was associated with differences in both fecal microbial concentrations and community composition.
The donkey was generally most distinct, with horse and zebra not differing.
Despite this, a common bacterial core of eight Operational Taxonomic Units (a definition used to classify groups together) 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.
“Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either, despite several taxa being prevalent and predominant.”
The core taxa shared by all the equine fecal samples numbered 70.
“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.”
The largest difference observed between the equine types was in terms of the anaerobic fungi. The six-fold higher anaerobic fungal concentrations in donkeys compared to horses is consistent with the reported higher fiber digestion ability of donkeys compared to horses, the researchers said.
Archaeal concentrations in donkeys and horse-donkey hybrids were both about two-fold higher compared to those in horses, which again points to their superior ability to digest fiber.
The authors said fecal samples are commonly used as a marker for the equine hindgut microbiota, as they can be obtained non-invasively. They say further work is needed to determine how the core microbiota in the hindgut of healthy equines is affected by diet.
Edwards, J.E., Shetty, S.A., van den Berg, P. et al. Animal microbiome (2020) 2: 6. https://doi.org/10.1186/s42523-020-0023-1