Individual virome analysis reveals the general co-infection of mammal-associated viruses with SARS-related coronaviruses in bats

We characterized the landscape of microorganisms in bat SARS-related coronavirus (SARSr-CoV) positive samples, including viruses, bacteria, and fungi in an individual bat anal swab for 76 bats using metagenomics analysis. We found a complexed microenvironment marked with the general co-circulation of microbes from two different sources: the mammal-associated viruses or the environment-associated microbes, the later includes the commensal bacteria, enterobacteria-related phage and the food-origin insect or fungi viruses.