Unravelling a Latent Pathobiome Across Coral Reef Biotopes

ABSTRACT Previous studies on disease in coral reef organisms have neglected the natural distribution of potential pathogens and the genetic factors that underlie disease incidence. This study explores the intricate associations between hosts, microbial communities, putative pathogens, antibiotic resistance genes (ARGs) and virulence factors (VFs) across diverse coral reef biotopes. We observed a substantial compositional overlap of putative bacterial pathogens, VFs and ARGs across biotopes, consistent with the ‘everything is everywhere, but the environment selects’ hypothesis. However, flatworms and soft corals deviated from this pattern, harbouring the least diverse microbial communities and the lowest diversity of putative pathogens and ARGs. Notably, our study revealed a significant congruence between the distribution of putative pathogens, ARGs and microbial assemblages across different biotopes, suggesting an association between pathogen and ARG occurrence. This study sheds light on the existence of this latent pathobiome, the disturbance of which may contribute to disease onset in coral reef organisms. We used shotgun metagenomic sequencing to assess microbiome composition and molecular markers for pathogenesis in 10 hosts and two non‐hosts (sediment and seawater) coral reef biotopes. This study uncovers the presence of a latent pathobiome in apparently healthy coral reef organisms.