title: Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov.
abstract: 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.
authors.affiliation: Laboratorium voor Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium.
authors.forename: Elke
authors.initials: E
authors.lastname: Vanlaere
authors.forename: Adam
authors.initials: A
authors.lastname: Baldwin
authors.forename: Dirk
authors.initials: D
authors.lastname: Gevers
authors.forename: Deborah
authors.initials: D
authors.lastname: Henry
authors.forename: Evie
authors.initials: E
authors.lastname: De Brandt
authors.forename: John J
authors.initials: JJ
authors.lastname: LiPuma
authors.forename: Eshwar
authors.initials: E
authors.lastname: Mahenthiralingam
authors.forename: David P
authors.initials: DP
authors.lastname: Speert
authors.forename: Chris
authors.initials: C
authors.lastname: Dowson
authors.forename: Peter
authors.initials: P
authors.lastname: Vandamme
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques; D001482:Base Composition; D019121:Burkholderia Infections / Q000382:microbiology / Q000662:veterinary; D042602:Burkholderia cepacia complex / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000502:physiology; D003550:Cystic Fibrosis / Q000382:microbiology*; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis; D005260:Female; D016680:Genome, Bacterial; D006801:Humans; D008413:Mastitis / Q000382:microbiology / Q000662:veterinary*; D009693:Nucleic Acid Hybridization; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D011938:Rec A Recombinases / Q000235:genetics; D017422:Sequence Analysis, DNA; D012756:Sheep; D012757:Sheep Diseases / Q000382:microbiology*; D013045:Species Specificity
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D011938:Rec A Recombinases