Uniqueness of Companion Animal Fecal Microbiota: Convergence Patterns Between Giant Pandas, Red Pandas, and Domesticated Animals

To investigate the influence of host ecological niche on fecal microbial community composition, this investigation employed high-throughput sequencing to characterize the microbiota composition in fecal samples. Giant pandas (GP), red pandas (RP), sympatric wildlife (SA), and domesticated animals (HA) in the Meigu Dafengding National Nature Reserve were used in the research. The research has found that GP bacteria are mainly composed of Proteobacteria and Pseudomonas, RP is enriched in Proteobacteria and Arthrobacter, SA is characterized by Firmicutes and Bacillus, and HA is dominated by Firmicutes and UCG-005 (uncultured Lachnospiraceae). In terms of fungi, GP and RP are mainly dominated by Ascomycota, enriched in Mrakia and Thelebolus, respectively, while SA is dominated by Ascomycota and Thelebolus, and HA is dominated by Chytridiomycota and Geotrichum. The assessment of alpha diversity demonstrated that HA had the highest microbial diversity and GP had the lowest; evaluation of beta diversity established that the community structures of each group were significantly separated. The study revealed a significant ecological divergence between the bacterial and fungal communities in sympatric wildlife, while giant pandas exhibit synergistic variation in their microbiota. This study provides new scientific basis for wildlife conservation from the perspective of focusing on microbial interactions.