Comparison of Fecal Microbiome of Wild Red Deer in Different Regions Reveals Geographic Differentiation

The gut microbiome plays critical roles in nutrient metabolism and host adaptation in ruminants, yet genome-level functional differences in the fecal microbiomes across geographic populations of wild red deer remain underexplored. Here, we integrated 16S rRNA gene sequencing and shotgun metagenomics to characterize the fecal microbiome of wild red deer populations in Inner Mongolia (NMG, n = 16) and Gansu Province (GS, n = 16), China. The NMG population exhibited significantly higher α-diversity and a distinct microbial community compared to GS (adjusted p < 0.05). NMG was enriched in Clostridium, Eubacterium, and Bacillus, while GS harbored higher abundances of Ruminococcus, Oscillospira, and Faecalibacterium (adjusted p < 0.05). Functional profiling revealed that the fecal microbiome in NMG showed greater functional potential associated with amino acid, pyruvate, and butanoate metabolism pathways, whereas the fecal microbiome in GS was enriched in the genetic potential of starch/sucrose metabolism, glycan degradation, and bile acid biotransformation (adjusted p < 0.05). CAZyme analysis demonstrated that GS was enriched in glycoside hydrolases, polysaccharide lyases, and carbohydrate esterases, while NMG showed higher auxiliary activity family abundance (adjusted p < 0.05). Genome-resolved metagenomics recovered 456 species-level genome bins (SGBs), revealing that GS-enriched SGBs (Rikenellaceae, Oscillospirales CAG-272) contained CAZyme genes associated with pectin degradation, whereas NMG-enriched SGBs contained genes associated with lignin modification and chitin degradation. These findings demonstrate the significant differences in the fecal microbiomes between the two geographically distinct wild red deer populations.