Metagenomic Analysis of Environmental Samples from Wildlife Rescue Station at Poyang Lake, China

Abstract

Objective

To improve the understanding of the virome and bacterial microbiome in the wildlife rescue station of Poyang Lake, China.

Methods

Ten smear samples were collected in March 2019 Metagenomic sequencing was performed to delineate bacterial and viral diversity. Taxonomic analysis was performed using the Kraken2 and Bracken methods. A maximum-likelihood tree was constructed based on the RNA-dependent RNA polymerase (RdRp) region of picornavirus.

Results

We identified 363 bacterial and 6 viral families. A significant difference in microbial and viral abundance was found between samples S01–S09 and S10. In S01–S09, members of Flavobacteriia and Gammaproteobacteria were the most prevalent, while in S10, the most prevalent bacteria class was Actinomycetia. Among S01–S09, members of Myoviridae and Herelleviridae were the most prevalent, while the dominant virus family of S10 was Picornaviridae. The full genome of the pigeon mesivirus-like virus (NC-BM-233) was recovered from S10 and contained an open reading frame of 8,124 nt. It showed the best hit to the pigeon mesivirus 2 polyprotein, with 84.10% amino acid identity. Phylogenetic analysis showed that RdRp clustered into Megrivirus B.

Conclusion

This study provides an initial assessment of the bacteria and viruses in the cage-smeared samples, broadens our knowledge of viral and bacterial diversity, and is a way to discover potential pathogens in wild birds