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1 Laboratorium voor Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
2 Department of Biological Sciences, Warwick University, Coventry CV4 7AL, UK
3 Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
4 Department of Pediatrics, University of Michigan, 1150 W. Medical Centre Drive, 8323 MRSB III, Box 0646, Ann Arbor, MI 48109-0646, USA
5 Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3TL, UK
Correspondence
Peter Vandamme
Peter.Vandamme{at}UGent.be
The aim of the present study was to re-examine the taxonomic position and structure of taxon K (also known as group K) within the Burkholderia cepacia complex (Bcc). For this purpose, a representative set of strains was examined by a traditional polyphasic taxonomic approach, by multilocus sequence typing (MLST) analysis and by analysis of available whole-genome sequences. Analysis of the recA gene sequence revealed three different lineages, designated recA-I, recA-II and recA-III. DNA–DNA hybridization experiments demonstrated that recA-I and recA-II isolates each represented a single novel species. However, DNA–DNA hybridization values of recA-II strains towards recA-III strains and among recA-III strains were at the threshold level for species delineation. By MLST, recA-I isolates were clearly distinguished from the others and represented a distinct lineage referred to as MLST-I, whereas recA-II and recA-III isolates formed a second MLST lineage referred to as MLST-II. A divergence value of 3.5 % was obtained when MLST-I was compared with MLST-II. The internal level of concatenated sequence divergence within MLST-I and MLST-II was 1.4 and 2.7 %, respectively; by comparison with the level of concatenated sequence divergence in established Bcc species, these data demonstrate that the MLST-I and MLST-II lineages represent two distinct species within the Bcc. The latter conclusion was supported by comparison of the whole-genome average nucleotide identity (ANI) level of MLST-I and MLST-II strains with strains of established Bcc species and by a whole-genome-based phylogenetic analysis. We formally propose to classify taxon K bacteria from the MLST-I and MLST-II lineages as Burkholderia contaminans sp. nov. (with strain J2956T =LMG 23361T =CCUG 55526T as the type strain) and Burkholderia lata sp. nov. (with strain 383T =ATCC 17760T =LMG 22485T =CCUG 55525T as the type strain), respectively. The MLST approach was confirmed as a valuable instrument in polyphasic taxonomic studies; more importantly, the cumulative data for about 1000 Bcc isolates analysed demonstrate that the 3 % concatenated sequence divergence level correlates with the 70 % DNA–DNA hybridization or 95 % whole-genome ANI threshold levels for species delineation.
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain R-15816 is AM905038, and those of the recA sequences of strains R-23139, R-15816, R-18442, R-20938, R-9896, R-18428, LMG 16227, LMG 23255 and LMG 23253 are respectively AM905032–AM905037 and AM922301–AM922303.
ANI values, G+C contents, DNA–DNA hybridization results and biochemical characteristics of the novel isolates and details of single-copy core genes used in tree reconstruction are available as supplementary material with the online version of this paper.
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