Comparative Analysis of Gastrointestinal Microbiota Along the Digestive Tract in Sika Deer and Reindeer and Prediction of Their Potential Function

Gastrointestinal microbiota are essential for fiber degradation, energy metabolism, nutrient utilization, and environmental adaptation in ruminants. Although sika deer and reindeer both belong to the family Cervidae, they differ in ecology, feeding habits, and digestive physiology, which may be reflected in their gastrointestinal microbiota. Here, we used 16S rRNA amplicon sequencing to characterize the gastrointestinal microbial communities of healthy 5-year-old male sika deer and reindeer, with particular attention to taxonomic composition, diversity patterns, and predicted functional profiles across anatomical segments. Both species were dominated by a limited number of highly abundant taxa, but clear interspecific differences were observed. At the phylum level, Bacillota and Bacteroidota predominated in both species, whereas Methanobacteriota was more abundant in reindeer and Bacillota was relatively more abundant in sika deer. At the genus level, methanogen-associated taxa were more prominent in reindeer, whereas Bacteroides, Prevotellaceae, and fiber-degradation-related taxa were more abundant in sika deer. Distinct segment-specific microbial patterns were observed along the gastrointestinal tract, especially among the foregut, small intestine, and hindgut. Alpha diversity varied across segments, whereas beta diversity showed clear separation among segments. Functional prediction indicated differences mainly in the overall structure of predicted functional profiles rather than in individual pathways. These findings provide baseline information for understanding gastrointestinal microecology and adaptive mechanisms in cervids.