Specific amino acid changes correlate with pathogenic flavobacteria

<i>Flavobacterium</i> is a genus of microorganisms living in a variety of hosts and habitats across the globe. Some species are found in fish organs, and only a few, such as <i>Flavobacterium psychrophilum</i> and <i>Flavobacterium columnare</i>, cause severe disease and losses in fish farms. The evolution of flavobacteria that are pathogenic to fish is unknown, and the protein changes accountable for the selection of their colonization to fish have yet to be determined. A phylogenetic tree was constructed with the complete genomic sequences of 208 species of the <i>Flavobacterium</i> genus using 861 softcore genes. This phylogenetic analysis revealed clade CII comprising nine species, including five pathogenic species, and containing the most species that colonize fish. Thirteen specific amino acid changes were found to be conserved across 11 proteins within the CII clade compared with other clades, and these proteins were enriched in functions related to replication, recombination, and repair. Several of these proteins are known to be involved in pathogenicity and fitness adaptation in other bacteria. Some of the observed amino acid changes can be explained by preferential selection for certain codons and tRNA frequency. These results could help explain how species belonging to the CII clade adapt to fish environments.