Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

Abstract

Background: Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed. Methods: We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering. Results: We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species. Conclusions: This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species. Reviewer: This article was reviewed by Dr. Xianwen Ren.

Comprehensive genome analysis of a pangolin-associatedParaburkholderia fungorumprovides new insights into its secretion systems and virulence

“…S1 ). The single marker gene approach may not be able to clearly differentiate all closely related members of Burkholderiales ( Jin et al, 2020 ). Therefore, we used a more robust and reliable whole-genome method or the core-genome SNP approach to further confirm the identity of the pangolin Pf ( Fig.…”

Discovery of a Novel Lineage Burkholderia cepacia ST 1870 Endophytically Isolated from Medicinal Polygala paniculata Which Shows Potent In Vitro Antileishmanial and Antimicrobial Effects

“…Members of this complex group exhibit genomes ranging from 7 to 9 Mbp, resulting in several taxonomic rearrangements [46,99], rapid mutation, and adaptation [102]. Bcc species exhibit high genetic International Journal of Microbiology International Journal of Microbiology similarity and is phenotypically indistinguishable [102][103][104], leading to often misidentifications interfering the effective treatment and epidemiological studies [52,105].…”

The Burkholderia genus: between mutualism and pathogenicity

“…Recientemente, Jin et al (2020) al usar el genoma completo de 116 cepas de Burkholderia, reportaron 36 genomovares dentro del CBC. Con base B. endofungorum were transferred to the new Paraburkholderia genus with Paraburkholderia graminis as a type species (Sawana et al, 2014).…”