Abstract
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.
Highlights
The gut microbiota of mammals provides the host with important functions, such as training the immune system early in life, metabolism, and synthesis of vitamins
We investigated the effects of domestication and captivity on the fecal microbiomes, as a proxy for the gastrointestinal microbiome, of a unique pair of horse populations living in Mongolia
Przewalski’s horse (PH) fecal microbiomes differ in composition and are more diverse compared to domesticated horses (Fig. 2)
Summary
As in comparative studies of fecal microbiomes from human populations[6], age had the most striking effect on horse fecal microbiome composition and diversity (Fig. 1, Figure S2). PH fecal microbiomes harbored a significantly higher relative abundance of Archeal methanogen Methanocorpusculum While these differences may be suggestive of PH and domestic horse gut microbiomes utilizing different gut metabolism pathways, we found that individuals from the two horse lineages consumed a similar level of plant diversity, yet differing compositions of plant taxa, as indicated by trnL gene maker molecular operational taxonomic units (MOTU) (Fig. 2c, Figure S4). We discovered that inter-individual variation was significantly lower in the PH population compared to the domestic population (Figure S7), which is similar to a trend discovered in gut microbiomes of a small human hunter-gatherer population in South America[2] Whether this trend is due to a less diverse host genetic pool or due to similar diets within the small host population is unknown. We suggest this could be a fruitful endeavor with possible health implications for the agricultural industry
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