Differences in Cecal Bacterial Communities and Predicted Functional Profiles Between Sympatric Subterranean and Aboveground Rodents

Gut microbiota contribute to host nutrition and metabolism, but their variation between sympatric rodents with contrasting lifestyles remains incompletely understood. We compared cecal bacterial communities of the Northeast China zokor (Myospalax psilurus) and Daurian ground squirrel (Spermophilus dauricus) from the meadow steppe of northeastern Inner Mongolia, China. Samples from 60 adults (30 per species; 13 males and 17 females) were analyzed using 16S rRNA gene sequencing. Major comparisons used Wilcoxon rank-sum tests, Bray–Curtis-based principal coordinate analysis with PERMANOVA, differential abundance analysis, and co-occurrence networks. Functional potential was inferred using PICRUSt2 and FAPROTAX. Chao1 richness was higher in M. psilurus (p < 0.001), whereas Shannon diversity did not differ significantly. Community structure differed between species (PERMANOVA, p < 0.001). Bacillota and Bacteroidota dominated both communities. Muribaculaceae-related taxa, [Eubacterium]_siraeum_group, and RF39-related taxa were more abundant in M. psilurus (Wilcoxon, p < 0.001), whereas Alistipes, Desulfovibrio, and Christensenellaceae-related taxa were more abundant in S. dauricus (Wilcoxon, p < 0.05). The S. dauricus network was more densely connected, whereas the M. psilurus network had higher modularity. PICRUSt2 predicted relative enrichment of carbohydrate metabolism and membrane transport in M. psilurus and amino acid metabolism in S. dauricus. These differences may be associated with species-specific ecological and physiological characteristics; the two-species comparison cannot isolate lifestyle effects. Direct dietary assessments, additional host species, and functional measurements are needed to clarify their biological significance.