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Several hypotheses exist regarding how specific bacteria can contribute towards the development of prostate cancer. Recovering microbial genomes, and their genomic features, from clinical samples and investigating fine-scale taxonomy is a critical first step in investigating causality. Here, we describe the microbial diversity of samples associated with prostate cancer. Metagenomic assembly of non-human reads from the PanProstate Cancer Group, derived from blood, saliva samples and prostate tissue whole-genome data (\n                    <jats:italic>N<\/jats:italic>\n                    \u2009=\u2009247), successfully reconstructed 249 highly complete bacterial genomes, predominantly from oral samples. Our data, reveals eighteen bacterial species from the oral cavity without species level classification, while demonstrating a wide range of known species. 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