Nanopore sequencing is a rapidly evolving technology useful for profiling communities of bacteria such as the oyster microbiome. By sequencing the rRNA operon (4200 + bp, Fig 1 ), species- and strain-level resolution can be achieved. Long-read methods provide a much more detailed picture of oyster microbiome dynamics, which can by obscured by short-read approaches that often limit resolution to the genus level or higher . For this study, extraction and sequencing methods were adapted for use on oysters reared in different settings, including semi-sterile lab conditions, an oyster farm, and wild or restored oyster reefs. The Oxford Nanopore MinION was used to profile rRNA operons and assess how the oyster microbiome varies geospatially, as well as the potential connections to oyster disease status (Perkinsus marinus infection). Phenomena observed at the species -level, such as the increase in Mycoplasma pulmonis in oysters moved to the common environment (Fig 2) , would be obscured at higher taxonomic levels (e.g. genus).