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Genome-based classification and identification of bacteria

Boris Vinatzer: Virginia Tech

<div>The number of sequenced bacterial genomes in public databases has surpassed the number of bacterial strains in culture collections. Although complete genome sequences offer the potential to precisely and correctly identify the associated bacteria, many of these genomes are assigned to the wrong species because of errors made by who submitted the genome sequences or subpar database curation. Moreover, even if all genomes in public databases were correctly identified at the species level, genomes of many beneficial or pathogenic plant-associated bacteria would still be of dubious identity. In fact, individual plant-associated bacterial species encompass vast genotypic and phenotypic diversity based on which isolates can be assigned to intraspecific classes such as pathovars, races, biovars, phylotypes, sequevars, clades, and many more. To address this immense challenge, we have designed LINbase, a database that automatically assigns genomes to genome similarity groups based on their Life Identification Numbers (LINs). These genome similarity groups can either be automatically associated with named species and intraspecific classes based on metadata of individual genomes or users can make these associations manually. The result is a tool that allows precise classification and identification of plant-associated bacteria at the species and intraspecific level with applications in plant biosecurity, plant disease diagnostics, and phytobiome research.</div>

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