Genomic identification of nitrogen-fixing Klebsiella variicola, K. pneumoniae and K. quasipneumoniae

被引:37
作者
Chen, Mingyue [1 ]
Li, Yuanyuan [1 ]
Li, Shuying [1 ]
Tang, Lie [1 ]
Zheng, Jingwu [1 ]
An, Qianli [1 ]
机构
[1] Zhejiang Univ, Inst Biotechnol, State Key Lab Rice Biol, Hangzhou 310058, Zhejiang, Peoples R China
基金
中国国家自然科学基金;
关键词
Average nucleotide identity; Klebsiella pneumoniae; Klebsiella quasipneumoniae; Klebsiella variicola; Nitrogen fixation; SEQUENCE; DNA; GENES; METABOLISM; CATABOLISM; DIVERSITY; FIXATION; BACTERIA; TAXONOMY; SYSTEM;
D O I
10.1002/jobm.201500415
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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. variicola 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.
引用
收藏
页码:78 / 84
页数:7
相关论文
共 26 条
[11]   Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola [J].
Garza-Ramos, Ulises ;
Silva-Sanchez, Jesus ;
Martinez-Romero, Esperanza ;
Tinoco, Perla ;
Pina-Gonzales, Marisol ;
Barrios, Humberto ;
Martinez-Barnetche, Jesus ;
Elena Gomez-Barreto, Rosa ;
Tellez-Sosa, Juna .
BMC MICROBIOLOGY, 2015, 15
[12]   DNA-DNA hybridization values and their relationship to whole-genome sequence similarities [J].
Goris, Johan ;
Konstantinidis, Konstantinos T. ;
Klappenbach, Joel A. ;
Coenye, Tom ;
Vandamme, Peter ;
Tiedje, James M. .
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2007, 57 :81-91
[13]   Genes for D-arabinitol and ribitol catabolism from Klebsiella pneumoniae [J].
Heuel, H ;
Shakeri-Garakani, A ;
Turgut, S ;
Lengeler, JW .
MICROBIOLOGY-SGM, 1998, 144 :1631-1639
[14]   Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health [J].
Holt, Kathryn E. ;
Wertheim, Heiman ;
Zadoks, Ruth N. ;
Baker, Stephen ;
Whitehouse, Chris A. ;
Dance, David ;
Jenney, Adam ;
Connor, Thomas R. ;
Hsu, Li Yang ;
Severin, Juliette ;
Brisse, Sylvain ;
Cao, Hanwei ;
Wilksch, Jonathan ;
Gorrie, Claire ;
Schultz, Mark B. ;
Edwards, David J. ;
Kinh Van Nguyen ;
Trung Vu Nguyen ;
Trinh Tuyet Dao ;
Mensinke, Martijn ;
Vien Le Minh ;
Nguyen Thi Khanh Nhu ;
Schultsz, Constance ;
Kuntaman, Kuntaman ;
Newton, Paul N. ;
Moore, Catrin E. ;
Strugnell, Richard A. ;
Thomson, Nicholas R. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (27) :E3574-E3581
[15]   MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform [J].
Katoh, K ;
Misawa, K ;
Kuma, K ;
Miyata, T .
NUCLEIC ACIDS RESEARCH, 2002, 30 (14) :3059-3066
[16]   Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains [J].
Kyrpides, Nikos C. ;
Hugenholtz, Philip ;
Eisen, Jonathan A. ;
Woyke, Tanja ;
Goeker, Markus ;
Parker, Charles T. ;
Amann, Rudolf ;
Beck, Brian J. ;
Chain, Patrick S. G. ;
Chun, Jongsik ;
Colwell, Rita R. ;
Danchin, Antoine ;
Dawyndt, Peter ;
Dedeurwaerdere, Tom ;
DeLong, Edward F. ;
Detter, John C. ;
De Vos, Paul ;
Donohue, Timothy J. ;
Dong, Xiu-Zhu ;
Ehrlich, Dusko S. ;
Fraser, Claire ;
Gibbs, Richard ;
Gilbert, Jack ;
Gilna, Paul ;
Glockner, Frank Oliver ;
Jansson, Janet K. ;
Keasling, Jay D. ;
Knight, Rob ;
Labeda, David ;
Lapidus, Alla ;
Lee, Jung-Sook ;
Li, Wen-Jun ;
Ma, Juncai ;
Markowitz, Victor ;
Moore, Edward R. B. ;
Morrison, Mark ;
Meyer, Folker ;
Nelson, Karen E. ;
Ohkuma, Moriya ;
Ouzounis, Christos A. ;
Pace, Norman ;
Parkhill, Julian ;
Qin, Nan ;
Rossello-Mora, Ramon ;
Sikorski, Johannes ;
Smith, David ;
Sogin, Mitch ;
Stevens, Rick ;
Stingl, Uli ;
Suzuki, Ken-ichiro .
PLOS BIOLOGY, 2014, 12 (08)
[17]  
Martínez J, 2004, INT MICROBIOL, V7, P261
[18]   Diazotrophic bacteria associated with banana (Musa spp.). [J].
Martínez, L ;
Caballero-Mellaod, J ;
Orozco, J ;
Martínez-Romero, E .
PLANT AND SOIL, 2003, 257 (01) :35-47
[19]   Shifting the genomic gold standard for the prokaryotic species definition [J].
Richter, Michael ;
Rossello-Mora, Ramon .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (45) :19126-19131
[20]   Klebsiella variicola, a novel species with clinical and plant-associated isolates [J].
Rosenblueth, M ;
Martínez, L ;
Silva, J ;
Martínez-Romero, E .
SYSTEMATIC AND APPLIED MICROBIOLOGY, 2004, 27 (01) :27-35