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.

哺乳动物肠道微生物组（gut microbiome）包含宿主微生物及其携带的全部基因，如今被视为宿主不可或缺的第二基因组，可为宿主提供关键生理功能。在人类中，已有研究表明生活方式会显著影响胃肠道微生物组的组成与多样性。我们据此推测，人类中存在的生活方式影响胃肠道微生物组组成与多样性的规律，在受到驯化、圈养等人为因素影响的哺乳动物类群中也同样成立——这类人为因素往往会大幅改变动物的饮食与自然生活史。本研究对两类马的粪便微生物组展开了探究：一类是目前全球仅存未被人类成功驯化的普氏野马（Przewalski’s horse, PH; Equus ferus przewalskii），另一类是栖息在相邻天然草原的放牧饲养家马（E. f. caballus）。研究发现，与家马相比，普氏野马的粪便微生物组拥有更为独特且多样的细菌群落，这一差异可部分通过trnL标记序列数据所揭示的植物饮食差异得到解释。在普氏野马种群内部，4只在欧洲动物园圈养出生的个体，其粪便微生物群落多样性显著低于法国与蒙古国自然保护区内出生的普氏野马个体。上述结果表明，人为因素可显著重塑马科动物的胃肠道微生物组，这一发现对濒危哺乳动物的保护管理具有更广泛的启示意义。