An enrichment approach for the recovery of viral and bacterial genomes from coral metagenomes

Abstract

Abstract Difficulties in obtaining viral and bacterial genomes from corals have hindered the mechanistic understanding of these holobionts. Here, we introduce a size-fractionation approach to enrich viruses and bacteria from coral samples (tissues, mucus, and skeleton) for metagenome sequencing. Enriched metagenomes reduced host and Symbiodium DNA from 70 to 36% while increasing bacterial recovery by 9-fold. Remarkably, bacterial metagenome-assembled genomes were only recovered from the enriched metagenomes, and viral genome recovery increased by 3-fold, expanding the diversity of viruses detected. The high recovery of viral and bacterial genomes described here will facilitate the expansion of functional genomic studies in coral holobionts.