Due to its filter feeding activities, the eastern oyster, Crassostrea virginica, has a high encounter rate with microbes in the seawater. While the oyster microbiome is distinct from the surrounding communities, challenges remain in understanding the complex host-microbiota environment interactions. 16S rRNA sequencing was used to profile the tissue-specific microbiomes, where a number of core taxa were identified along with a subset of taxa showing differential abundance upon infection by the protozoan pathogen Perkinsus marinus. Functional studies of the digestive tract microbiome was performed using shotgun metagenomic sequencing, where metagenome assembled genomes (MAGs) representing uncultured strains of Mollicutes and Chlamydiae were assembled. Detailed functional analysis of the MAGs revealed genes involved in potential host associations. Further study of eastern oyster-microbe interactions will enable our understanding of the role of microbiomes in host population dynamics.