AUTHOR=Peeters Charlotte , De Canck Evelien , Cnockaert Margo , De Brandt Evie , Snauwaert Cindy , Verheyde Bart , Depoorter Eliza , Spilker Theodore , LiPuma John J. , Vandamme Peter 

TITLE=Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism

JOURNAL=Frontiers in Microbiology

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.02556

DOI=10.3389/fmicb.2019.02556

ISSN=1664-302X

ABSTRACT=<p>Comparative analysis of partial <italic>gyrB</italic>, <italic>recA</italic>, and <italic>gltB</italic> gene sequences of 84 <italic>Pandoraea</italic> reference strains and field isolates revealed several clusters that included no taxonomic reference strains. The <italic>gyrB</italic>, <italic>recA</italic>, and <italic>gltB</italic> phylogenetic trees were used to select 27 strains for whole-genome sequence analysis and for a comparative genomics study that also included 41 publicly available <italic>Pandoraea</italic> genome sequences. The phylogenomic analyses included a Genome BLAST Distance Phylogeny approach to calculate pairwise digital DNA–DNA hybridization values and their confidence intervals, average nucleotide identity analyses using the OrthoANIu algorithm, and a whole-genome phylogeny reconstruction based on 107 single-copy core genes using bcgTree. These analyses, along with subsequent chemotaxonomic and traditional phenotypic analyses, revealed the presence of 17 novel <italic>Pandoraea</italic> species among the strains analyzed, and allowed the identification of several unclassified <italic>Pandoraea</italic> strains reported in the literature. The genus <italic>Pandoraea</italic> has an open pan genome that includes many orthogroups in the ‘Xenobiotics biodegradation and metabolism’ KEGG pathway, which likely explains the enrichment of these species in polluted soils and participation in the biodegradation of complex organic substances. We propose to formally classify the 17 novel <italic>Pandoraea</italic> species as <italic>P. anapnoica</italic> sp. nov. (type strain LMG 31117<sup>T</sup> = CCUG 73385<sup>T</sup>), <italic>P. anhela</italic> sp. nov. (type strain LMG 31108<sup>T</sup> = CCUG 73386<sup>T</sup>), <italic>P. aquatica</italic> sp. nov. (type strain LMG 31011<sup>T</sup> = CCUG 73384<sup>T</sup>), <italic>P. bronchicola</italic> sp. nov. (type strain LMG 20603<sup>T</sup> = ATCC BAA-110<sup>T</sup>), <italic>P. capi</italic> sp. nov. (type strain LMG 20602<sup>T</sup> = ATCC BAA-109<sup>T</sup>), <italic>P. captiosa</italic> sp. nov. (type strain LMG 31118<sup>T</sup> = CCUG 73387<sup>T</sup>), <italic>P. cepalis</italic> sp. nov. (type strain LMG 31106<sup>T</sup> = CCUG 39680<sup>T</sup>), <italic>P. commovens</italic> sp. nov. (type strain LMG 31010<sup>T</sup> = CCUG 73378<sup>T</sup>), <italic>P. communis</italic> sp. nov. (type strain LMG 31110<sup>T</sup> = CCUG 73383<sup>T</sup>), <italic>P. eparura</italic> sp. nov. (type strain LMG 31012<sup>T</sup> = CCUG 73380<sup>T</sup>), <italic>P. horticolens</italic> sp. nov. (type strain LMG 31112<sup>T</sup> = CCUG 73379<sup>T</sup>), <italic>P. iniqua</italic> sp. nov. (type strain LMG 31009<sup>T</sup> = CCUG 73377<sup>T</sup>), <italic>P. morbifera</italic> sp. nov. (type strain LMG 31116<sup>T</sup> = CCUG 73389<sup>T</sup>), <italic>P. nosoerga</italic> sp. nov. (type strain LMG 31109<sup>T</sup> = CCUG 73390<sup>T</sup>), <italic>P. pneumonica</italic> sp. nov. (type strain LMG 31114<sup>T</sup> = CCUG 73388<sup>T</sup>), <italic>P. soli</italic> sp. nov. (type strain LMG 31014<sup>T</sup> = CCUG 73382<sup>T</sup>), and <italic>P. terrigena</italic> sp. nov. (type strain LMG 31013<sup>T</sup> = CCUG 73381<sup>T</sup>).</p>