Diet contributes to microbiome and niche differentiation among three sympatric cervids

Niche differentiation is a fundamental mechanism facilitating the coexistence of sympatric species, yet the extent to which dietary partitioning is associated with gut microbial differentiation remains poorly understood in wild cervids.

Here, we investigated winter dietary composition and fecal microbiome communities of three sympatric cervid species-moose (Alces alces), red deer (Cervus elaphus), and roe deer (Capreolus pygargus)-in Youhao National Nature Reserve, northeastern China. A total of 55 fresh fecal samples were collected in January 2024, including 19 moose, 7 red deer, and 29 roe deer samples. Dietary composition was characterized using rbcL DNA metabarcoding, while microbiome communities were assessed using full-length 16S rRNA gene sequencing.

Our results showed the three cervid species exhibited distinct dietary patterns, moose showed a relatively narrow woody-plant-dominated diet, whereas red deer and roe deer exhibited higher dietary diversity, and roe deer exhibited broader use of shared plant resources; microbiome communities also differed significantly among host species, with moose showing the clearest separation from red deer and roe deer in community composition and predicted microbial metabolic potentials; Procrustes analysis revealed significant concordance between dietary composition and microbiome community, and redundancy analysis also indicated that dietary plant composition explained a significant proportion of variation in microbiome community.

These findings demonstrate that trophic differentiation among sympatric cervids is accompanied by coordinated variation in gut microbial community structure and predicted functional potential. The results support a close ecological association between dietary niche differentiation and host-associated microbiome variation, while causal and directional mechanisms require confirmation through longitudinal, experimental, and direct functional studies.