Comparison and association of winter diets and gut microbiota using trnL and 16S rRNA gene sequencing for three herbivores in Taohongling, China

Food provides essential nutrients and energy for wildlife and directly influences the compositional patterns of the gut microbiota in natural reservoirs. Little is known about the interspecific differences and correlations between diet and microbial communities in sympatric herbivores. We conducted chloroplast trnL and 16S rRNA genes amplicon sequencing of 90 faecal samples from sika deer (Cervus nippon kopschi), Reeve's muntjac (Muntiacus reevesi), and a Chinese hare (Lepus sinensis). Diet analysis revealed that sika deer predominantly foraged on Rubus (36.5 %), Loropetalum (25.5 %), and Eurya (13.4 %) at the genus level; Reeve's muntjac favoured Rubus (51.8 %), Eurya (11.0 %), and Euonymus (6.1 %); Chinese hare showed dominance in Rubus (15.8 %), Smilax (15.6 %), and Rhus (10.6 %) consumption, with all these forage plants being shrubs. The gut microbiota of the three herbivores was characterised by Firmicutes, Bacteroidetes, and Proteobacteria, although the relative abundances of these taxa differed across herbivore species. Alpha diversity indicated no significant differences between sika deer and Reeve's muntjac, whereas alpha indices showed significant differences between sika deer and Chinese hare (p < 0.05). Beta diversity analysis indicated significant differences between the Chinese hare and sika deer, as well as between the Chinese hare and Reeve's muntjac (p < 0.05), with no significant difference found between the two cervid species, which may be attributed to the influence of interspecific genetics and evolutionary factors. Due to seasonal shifts, the food availability for herbivores decreased, resulting in the convergent adaptation of shrubs consumed by the three species. Furthermore, PICRUSt functional profile prediction indicated that the gut microbiota of the three species were mainly enriched in metabolic functions. Mantel correlation analysis suggested that the gut microbiota of sika deer showed a significant positive correlation with five genera of plants, one genus of Reeve's muntjacs, and three genera of Chinese hare (p < 0.01), suggesting that the gut microbiota of sika deer may be more susceptible to changes in food abundance. Our study emphasises how the winter climate affects the foraging strategies and microbial communities of the three herbivores, as well as their correlations. These results may further contribute to the food selection, regulation of gut microbiota, disease prevention, conservation, and management of sika deer and other sympatric herbivores.