Kitchen waste and dry-toilet exposure are likely associated with gut microbiota shifts, pathogen-associated taxa, and lipid metabolism-related functional potential in wild white-lipped deer in Xizang, China

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Abstract Human disturbances significantly impact wildlife gut microbiota. Using metagenomic sequencing, we compared gut microbiota structure and lipid metabolism between two wild white-lipped deer populations on the Qinghai-Tibet Plateau: GBJD, where deer were observed consuming high-fat kitchen waste and licking feces-urine mixtures from dry toilets, and ND, without these behaviors. There were significant differences in gut microbiota structure and lipid metabolism between populations. GBJD exhibited a roughly twofold higher Firmicutes-to-Bacteroidetes ratio than in ND and marked beta-diversity separation. LEfSe analysis revealed Arthrobacter and Rhodococcus had significantly higher relative abundances in GBJD, while Bacteroidota and Bacteroides had significantly higher relative abundances in ND. Furthermore, the relative abundances of several pathogen-associated taxa were significantly higher in GBJD than in ND. Importantly, relative abundances of fatty acid degradation and biosynthesis pathways and beta-oxidation-related enzymes were significantly higher in GBJD than in ND. These differences may be associated with differing anthropogenic conditions, as white-lipped deer in GBJD were observed consuming high-fat kitchen waste and licking human feces–urine mixtures from dry toilets, potentially increasing food availability and exposure to human-associated microbes. This study highlights the need for closed management of kitchen waste and dry toilets to reduce wildlife access and potential human–wildlife–livestock transmission risks.

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