Data from: Evaluating the impact of domestication and captivity on the horse gut microbiome

The mammal gut microbiome, which includes host microbes and their
respective genes, is now recognized as an essential second genome that
provides critical functions to the host. In humans, studies have revealed
that lifestyle strongly influences the composition and diversity of the
gastrointestinal microbiome. We hypothesized that these trends in humans
may be paralleled in mammals subjected to anthropogenic forces such as
domestication and captivity, in which diets and natural life histories are
often greatly modified. We investigated fecal microbiomes of Przewalski’s
horse (PH; Equus ferus przewalskii), the only horses alive today not
successfully domesticated by humans, and herded, domestic horse (E. f.
caballus) living in adjacent natural grasslands. We discovered PH fecal
microbiomes hosted a distinct and more diverse community of bacteria
compared to domestic horses, which is likely partly explained by different
plant diets as revealed by trnL maker data. Within the PH population, four
individuals were born in captivity in European zoos and hosted a
strikingly low diversity of fecal microbiota compared to individuals born
in natural reserves in France and Mongolia. These results suggest that
anthropogenic forces can dramatically reshape equid gastrointestinal
microbiomes, which has broader implications for the conservation
management of endangered mammals.