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Genomic identification of nitrogen‐fixing Klebsiella variicola , K. pneumoniae and K. quasipneumoniae
Author(s) -
Chen Mingyue,
Li Yuanyuan,
Li Shuying,
Tang Lie,
Zheng Jingwu,
An Qianli
Publication year - 2016
Publication title -
journal of basic microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.58
H-Index - 54
eISSN - 1521-4028
pISSN - 0233-111X
DOI - 10.1002/jobm.201500415
Subject(s) - biology , genome , genetics , operon , comparative genomics , gene , klebsiella pneumoniae , whole genome sequencing , escherichia coli , genomics
It was difficult to differentiate Klebsiella pneumoniae , K. quasipneumoniae and K. variicola by biochemical and phenotypic tests. Genomics increase the resolution and credibility of taxonomy for closely‐related species. Here, we obtained the complete genome sequence of the K. variicol a type strain DSM 15968 T (=F2R9 T ). The genome of the type strain is a circular chromosome of 5,521,203 bp with 57.56% GC content. From 540 Klebsiella strains whose genomes had been publicly available as at 3 March 2015, we identified 21 strains belonging to K. variicola and 8 strains belonging to K. quasipneumoniae based on the genome average nucleotide identities (ANI). All the K. variicola strains, one K. pneumoniae strain and five K. quasipneumoniae strains contained nitrogen‐fixing genes. A phylogenomic analysis showed clear species demarcations for these nitrogen‐fixing bacteria. In accordance with the key biochemical characteristics of K. variicola , the idnO gene encoding 5‐keto‐D‐gluconate 5‐reductase for utilization of 5‐keto‐D‐gluconate and the sorCDFBAME operon for catabolism of L‐sorbose were present whereas the rbtRDKT operon for catabolism of adonitol was absent in the genomes of K. variicola strains. Therefore, the genomic analyses supported the ANI‐based species delineation; the genome sequence of the K. variicola type strain provides the reference genome for genomic identification of K. variicola , which is a nitrogen‐fixing species.