The gut microbiota of Brandt’s vole under varying population densities reveals contrasting patterns in the natural environment

The population density of rodents fluctuates due to intrinsic and extrinsic factors, inducing density-dependent effects on organisms and their habitats. The gut microbiota of herbivores plays a pivotal role in digestion, immunity, environmental adaptation, and host fitness. Crowding and host population density are considered among the driving factors that influence the gut microbiome of rodents. In laboratory settings, the gut microbiome of Brandt’s voles exhibits distinct responses to density and crowding, which is a controlled environment and cannot mimic the natural system; however, its response in natural settings remains underexplored, which is more complex and shaped by biotic and abiotic interactions. Our study provides a comprehensive profiling of the ( Lasiopodomys brandtii ) gut microbiome at various population densities, under natural conditions, where diet and social structure fluctuate dynamically. Across all densities, the dominant bacterial phyla were Firmicutes, Bacteroidota, Desulfobacterota, Campylobacterota, Actinobacteriota, and Patescibacteria. The Patescibacteria were significantly lower at medium (0.57% ± 0.117) and high densities (0.65% ± 0.423) than at low density (0.93% ± 0.339), whereas the Proteobacteria were higher at medium density (0.84% ± 0.518) than at low (0.43% ± 0.18) and high (0.54% ± 0.34) densities. Clostridia_vadinBB60 and F082 were reduced at high density relative to low and medium densities, and Lactobacillus abundance was lower at medium density compared with low and high densities. The microbial biomarkers at each density were ( p < 0.05, LDA > 3): (Low; Bacilli , Helicobacter , Clostridiales_vadinBB60 , F082 , and Saccharimonadia ), (Medium; Christensenellaceae ), (High; Lactobacillus , Prevotella, and Lachnospiraceae ). Alpha diversity was significantly lower at high density than at low and medium densities. At high density, Pielou's evenness, Shannon diversity index, observed richness, and Simpson's diversity were significantly lower than at low and medium densities ( p < 0.05). Community structure differed significantly between low and high densities and between medium and high densities, but was similar between low and medium densities ( p < 0.05). Bacterial predicted functional pathways varied significantly between low and medium densities and between high and medium densities, but showed no differences between low and high densities ( p < 0.05). Density, AP, and pH were primary drivers of variance in microbial communities ( p < 0.05). Mantel tests show that gut microbial diversity of voles is significantly correlated with density ( r = 0.26, p = 0.0006) and water content ( r = 0.19, p = 0.025), and microbial abundance is associated with soil water content ( r = 0.26, p = 0.001) and aboveground biomass (AGB) ( r = 0.24, p = 0.001). Density negatively affects microbial communities while positively affecting the soil physicochemical factors. This study demonstrates that host population density serves as the primary driver of variation in gut microbiome in wild Brandt's voles. Soil properties and plant biomass act as secondary environmental filters. This work underscores the central role of host population dynamics in shaping the gut microbiome in natural systems, with potential implications for understanding how crowding stress influences host–microbe interactions in wild small mammals.