Seasonal covariations of diet-gut microbiota in the adaptation of the newly reintroduced Père David's deer (Elaphurus davidianus) to the northern habitat

Milu (Père David's deer, Elaphurus davidianus), once extinct in the wild, was one of the few indigenous large herbivores of the wetland ecosystem in China. The reintroduction of milu in northern China has just started and is expected to restore not only that species, but also the ecosystem. To acquire insights into the adaptive process of the milu population first rewilded in the northern habitat and provide knowledge for the on-going and future reintroduction attempts, we used DNA metabarcoding to analyze the diets and gut microbiota of those milu in the first year after releasing. The results showed strong seasonality in both diet and gut microbiota. Significant higher dietary diversity was detected in in autumn than summer and winter. Woody dietary components increased continuously from summer to winter. A significant correspondence was found between the dietary and microbial diversities. Enrichment of metabolic pathways involved in lipid and amino acid metabolism was identified in summer, and of those involved in carbohydrate and glycan metabolism was identified in winter. Pathways related to metabolism of certain amino acid were differently abundant in the breeding season. The study indicated the contribution of foraging and gut microbial seasonality to the overwintering, reproduction and environmental adaption of the reintroduced milu. The enrichment of opportunistic pathogen Treponema and lower microbial diversity indicated higher health risk in winter, and thus disease prevention measures were suggested. Pre- and post-release food evaluation and monitoring was recommended to ensure food sufficiency in the reintroductions.