A targeted approach to enrich host-associated bacteria for metagenomic sequencing

Multicellular eukaryotic organisms are hosts to complex communities of bacteria that reside on or inside their tissues. Often the eukaryotic members in complex communities contribute to high proportions of metagenomic sequencing reads, making it challenging to achieve sufficient sequencing depth to evaluate bacterial ecology. Stony corals are one such complex community; however, separation of bacterial from eukaryotic (primarily coral and algal symbiont) cells has so far not been successful. Using a combination of hybridization chain reaction fluorescence in situ hybridization and fluorescence activated cell sorting (HCR-FISH + FACS), we sorted two populations of bacteria from five genotypes of the coral Acropora loripes, targeting 1) Endozoicomonas spp, and 2) all other bacteria. These are the raw reads for this data set.