Comparative metagenomic analysis reveals shared dominant microbiota and differential metabolic potential in captive sika deer and fallow deer

Captive conditions and shared diets may constrain gut microbial variation among host species, while residual differences may reflect species-associated patterns under the studied captive conditions. Sika deer ( Cervus nippon ) and fallow deer ( Dama dama ) are both cervids maintained under comparable zoo conditions, providing a useful model for examining whether microbiome differences persist when environmental variation is minimized. We characterized the fecal microbiota of 22 adult deer housed at Yinchuan City Zoo, including sika deer and fallow deer, using shotgun metagenomic sequencing. Firmicutes and Bacteroidetes dominated both groups, indicating a shared dominant phylum. Fallow deer exhibited higher Shannon diversity, whereas the other diversity indices showed no significant differences. Overall community structure showed substantial overlap between groups, with no significant separation detected by complementary statistical analyses. Nevertheless, specific bacterial and archaeal taxa differed between the two deer groups, and pathways related to allantoin, amino acid, glycosaminoglycan, and bioactive amine metabolism showed differential enrichment. Because several pathway differences were significant only before multiple-testing correction, they should be regarded as exploratory candidate functional signals requiring further validation. Overall, the two deer species shared a conserved fecal microbiome and basic functional framework, with between-group differences mainly involving specific microbial taxa and candidate metabolic pathways under the studied captive conditions.