The Gut Microbiota of Young Asian Elephants with Different Milk-Containing Diets

SIMPLE SUMMARY: Insufficient maternal milk is one of the important reasons for the low survival rate of young Asian elephants. Finding the optimal break milk supplementation for young Asian elephants is a matter of urgency. In our study, we investigated the microbiomes of young Asian elephants on different milk-containing diets (elephant milk only, elephant milk–plant mixed feed, and goat milk–plant mixed feed). Our results suggested that goat milk is not suitable for young elephants, and yak milk may be an ideal source of supplemental milk for Asian elephants. ABSTRACT: Evaluating the association between milk-containing diets and the microbiomes of young Asian elephants could assist establishing optimal breast milk supplementation to improve offspring survival rates. The microbiomes of young Asian elephants on different milk-containing diets (elephant milk only, elephant milk–plant mixed feed, and goat milk–plant mixed feed) were investigated using high-throughput sequencing of 16S rRNA genes and phylogenetic analysis. Microbial diversity was lower in the elephant milk-only diet group, with a high abundance of Proteobacteria compared to the mixed-feed diet groups. Firmicutes and Bacteroidetes were dominant in all groups. Spirochaetae, Lachnospiraceae, and Rikenellaceae were abundant in the elephant milk–plant mixed-feed diet group, and Prevotellaceae was abundant in the goat milk–plant mixed-feed diet group. Membrane transport and cell motility metabolic pathways were significantly enriched in the elephant milk–plant mixed-feed diet group, whereas amino acid metabolism and signal transduction pathways were significantly enriched in the goat milk–plant mixed-feed diet group. The intestinal microbial community composition and associated functions varied significantly between diets. The results suggest that goat milk is not suitable for young elephants. Furthermore, we provide new research methods and directions regarding milk source evaluation to improve elephant survival, wellbeing, and conservation.