Tetrodotoxin (TTX) is a potent neurotoxin found in phylogenetically diverse organisms, including marine invertebrates, molluscs and fish, as well as terrestrial amphibians. This diversity of source has prompted speculation that TTX is produced by bacteria or other microscopic organisms taken up by the hosts, rather than by the host per se. Currently >150 species of bacteria have been described as ‘TTX-producers’ in the literature. We will therefore perform metagenomic WGS on microbial communities associated with a single marine host, Pacific oysters, which we found accumulates TTX in a reproducible season-dependent manner at our field site. This allows us to focus on the changes in microbial communities within a single host as it transitions from a TTX-negative to a TTX-positive state, and back. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/