design: Farmed eastern oysters were collected from Ninigret Pond, Rhode Island (USA). Gut samples from 10 oysters were pooled together and homogenized. The homogenate was processed through multiple rounds of centrifugation to reduce the presence of host cells. The supernatant was pushed through a 3 micrometer pore size filter with a syringe. Then, the flow through was pushed through a 0.2 micrometer pore size filter to capture host-associated microbes in the 0.2-3 micrometer size fraction. Genomic DNA was extracted from the 0.2 micrometer pore size filter with a QIAGEN QIAamp PowerFecal DNA Kit. Library preparation was performed at the Rhode Island Genomics and Sequencing Center with a Wafergen Apollo 324 with PrepX reagents. The resultant library underwent paired-end sequencing on an Illumina NextSeq 500 platform (Mid-output, 2x150 bp) at Duke Universitys Sequencing and Genomic Technologies Core.