| Summary: | The genus <i>Flavobacterium</i> contains a large group of commensal bacteria identified in diverse terrestrial and aquatic habitats. We compared the genome of a new species <i>Flavobacterium akiainvivens</i> IK-1<sup>T</sup> to public available genomes of <i>Flavobacterium</i> species to reveal the genomic traits and ecological roles of IK-1<sup>T</sup>. Principle component analysis (PCA) of carbohydrate-active enzyme classes suggests that IK-1<sup>T</sup> belongs to a terrestrial clade of <i>Flavobacterium</i>. In addition, type 2 and type 9 secretion systems involved in bacteria-environment interactions were identified in the IK-1<sup>T</sup> genome. The IK-1<sup>T</sup> genome encodes eukaryotic-like domain containing proteins including ankyrin repeats, von Willebrand factor type A domain, and major royal jelly proteins, suggesting that IK-1<sup>T</sup> may alter plant host physiology by secreting eukaryotic-like proteins that mimic host proteins. A novel two-component system <i>Fa</i>RpfC-<i>Fa</i>YpdB was identified in the IK-1<sup>T</sup> genome, which may mediate quorum sensing to regulate global gene expressions. Our findings suggest that comparative genome analyses of <i>Flavobacterium</i> spp. reveal that IK-1<sup>T</sup> has adapted to a terrestrial niche. Further functional characterizations of IK-1<sup>T</sup> secreted proteins and their regulation systems will shed light on molecular basis of bacteria-plant interactions in environments.
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