Microbiome Composition and Functional Shifts in Wild Mammals Exposed to Anthropogenic Environmental Disturbances

Abstract

This study evaluated the impact of human-driven environmental disturbances on the composition and functional capabilities of the mammalian gut microbiota at different environmental disturbance gradients. This study attempted to determine the effect that human activities like urbanization, habitat fragmentation, intensified agriculture, pollution, and habitat invasion have on microbial diversity, taxonomic composition, and predicted metabolic pathways related to host physiology and adaptation. Fecal samples were collected from wild mammals living in forests, agricultural lands, and urban environments. 16S rRNA gene amplicon sequencing was done to analyze the microbial composition. Microbial diversity was analyzed based on alpha diversity, beta diversity, microbial taxonomy, and functional pathway prediction using bioinformatics pipeline. Environmental factors such as vegetation cover, pollution levels, habitat fragmentation, and human activity levels were incorporated into microbial community data. PERMANOVA tests, correlation analysis, and random forest models were used to identify microbial biomarkers in response to environmental disturbances. Around 9.4 million high-quality reads produced 3,286 ASVs. Microbial diversity declined significantly along the disturbance gradient, with Shannon diversity decreasing from 5.86 ± 0.24 in forest habitats to 4.28 ± 0.18 in urban habitats (p < 0.001). Observed ASVs declined from 842 ± 65 to 548 ± 47. Firmicutes abundance decreased from 48.3% to 35.6%, while Proteobacteria increased from 8.7% to 22.4% in urban environments. Functional analyses revealed enrichment of xenobiotic degradation pathways (4.1% to 14.6%), stress-response mechanisms (5.3% to 16.2%), and antimicrobial resistance genes (2.8% to 11.4%). PERMANOVA confirmed significant microbial community differentiation among habitats (R² = 0.31, p < 0.001). Anthropogenic environmental disturbances significantly reshape wildlife microbiomes by reducing microbial diversity and promoting stress-adapted microbial functions. Microbiome-based indicators may therefore serve as valuable tools for ecosystem monitoring, wildlife conservation, and environmental health assessment in increasingly
human-modified landscapes.