Gut microbiome reveals contrasting enterotypes and health statuses of semi-wild Saiga antelopes (Saiga tatarica)

Gut microbiome studies based on fecal samples can non-invasively reflect the survival and health status of endangered species. This study presents the first characterization of the gut microbiome in the semi-wild population of the critically endangered Saiga antelope (Saiga tatarica), unveiling the existence of two distinct enterotypes within the semi-wild Saiga: the Oscillospiraceae UCG-005 enterotype and the Arthrobacter enterotype. These enterotypes show significant differences in microbiome diversity, composition, and predicted functions. The Arthrobacter enterotype has lower alpha diversity, fewer short-chain fatty acids (SCFAs)-producing bacteria, more potential pathogens, lower energy metabolism and higher lipid metabolism abundance. The findings imply that Saiga with the Arthrobacter enterotype have lower energy utilization efficiency and higher disease risks, particularly for obesity. Microbial correlation network analysis indicates SCFAs-producing bacteria play a key role in the formation of these enterotypes. This suggests that next-generation probiotics, primarily composed of SCFAs-producing bacteria, could be used to regulate and improve the health of the Saiga. Additionally, the similarity of the enterotype associated with a healthier survival state to that of wild counterparts suggests that incorporating gut microbiome monitoring into the key indicators for the reintroduction of endangered species could be significant for wildlife conservation and management.