Comparison of gut viromes from different species of mammals in zoos unveiled the genetic diversity of bacteriophage dark matter and mammalian viruses

The mammalian gut viromes contain various commensal and potential zoonotic viruses, and thus the continuous monitoring of the gut virome in domestic and wild mammals is necessary to mitigate any potential zoonotic spillover incident. Using viral metagenomic analysis, the gut viral communities in zoo mammals kept in different zoos in China were investigated. Our results revealed significant differences in viral communities across mammals with distinct feeding habits, and the herbivores exhibited the highest viral species diversity. Totally, 1,027 viral sequences, belonging to five major viral groups, were generated, and several mammal-infecting viruses with potential infectivity were identified, including astroviruses, picornaviruses and parvoviruses. The phylogenetic trees based on the virus hallmark genes revealed that these viral genomes presented highly genetic diversity. And the host of most microviruses were predicted to belong to the bacterial family Bacteroidaceae. Besides, ten previously undiscovered crAss-like phages were identified in mammals and showed a close relationship to the proposed crAssphages in human gut virome. The antibiotic resistance genes (ARGs) in the mammal gut viromes mainly belonged to tetracyclines. This work greatly enhances our knowledge of viral communities in zoo animals in China, contributing to the preventive surveillance for potential zoonotic mammalian viruses.