Systematic Taxonomy Of Bacteria Belonging To The Genus Kosakonia Based On The Whole Genome Sequences

The genus Kosakonia was recently divided from the genus Enterobacter in the family Enterobacteriaceae. Except that the type species K. cowanii was isolated from human, the other species of the genus Kosakonia are associated with plants. Except the known K. radicincitans strain YD4, most of Kosakonia members are able to promote plant growth. The taxonomic status of some members of the genus Kosakonia was not clear. The objective of this study was to clarify the taxonomic status using taxono-genomic methods.The genome sequences of five type strains (K. cowanii DSM 18146T, K. oryzae Ola51T, K. arachidis DSM 25165T, E. oryziphilus LMG 26429T, E. oryzendophyticus LMG 26432T) were sequenced using the PacBio SMRT technology and the complete genome sequences were obtained.The genome relatedness of 11 strains (K. cowanii DSM 18146T, K. oryzae Ola51T, K. arachidis DSM 25165T, E. oryziphilus LMG 26429T, E. oryzendophyticus LMG 26432T, K. radicincitans DSM 16656T, K. radicincitans UMEnt01/12, K. radicincitans YD4, Kosakonia sacchari SP1T, Kosakonia oryzae KO348 and Enterobacter sp. R4-368) was analyzed using the new methods of OrthoANI (Orthologous Average Nucleotide Identity) and MiSI (Microbial Species Identifier). The results revealed that the K. oryzae strain Ola51T belongs to the species K. radicincitans, the strain K0348 formerly belonging to the species K. oryzae and the strain R4-368 represent a novel species closely related to K. sacchari, and E. oryziphilus is closely related to K. arachidis.Phylogenetic analyses based on the 16S rRNA gene sequences and the amino acid sequences encoding by the core genomes of the genus Kosakonia and the closely related genera Enterobacter, Citrobacter and Cronobacter showed that the 11 strains were monophyletic, likely belonging to the same genus, and formed 4 phylogenetic groups.The threshold values of ANI and POCP (percentage of conserved proteins) for demarcating the genera of Kosakonia, Enterobacter, Citrobacter and Cronobacter and the taxonomic status of K. cowanii have not been clearly determined because the taxonomic status of some members of the genera Enterobacter and Citrobacter is not clear and the numbers of whole genome sequences of the type strains are not enough.Genomic analysis showed that the 11 members of the genus Kosakonia contain genes related to plant growth-promotion or plant pathogenicity. They thus have the potential of promoting plant growth or causing plant disease. Their genotypes are correlated to their phylogenetic relationships. K. cowanii shows genotypic differences from other members of the genus Kosakonia.This study provided five complete genome sequences for systemic studies of evolution and genetics of the genus Kosakonia and clarified the taxonomic status of most members of the genus Kosakonia.