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Comparative genomics of Pandoraea, a genus enriched in xenobiotic biodegradation and metabolism

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Abstract
Comparative analysis of partial gyrB, recA, and gltB gene sequences of 84 Pandoraea reference strains and field isolates revealed several clusters that included no taxonomic reference strains. The gyrB, recA, and gltB 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 Pandoraea 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 Pandoraea species among the strains analyzed, and allowed the identification of several unclassified Pandoraea strains reported in the literature. The genus Pandoraea 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 Pandoraea species as P. anapnoica sp. nov. (type strain LMG 31117(T) = CCUG 73385(T)), P. anhela sp. nov. (type strain LMG 31108(T) = CCUG 73386(T)), P. aquatica sp. nov. (type strain LMG 31011(T) = CCUG 73384(T)), P. bronchicola sp. nov. (type strain LMG 20603(T) = ATCC BAA-110(T)), P. capi sp. nov. (type strain LMG 20602(T) = ATCC BAA-109(T)), P. captiosa sp. nov. (type strain LMG 31118(T) = CCUG 73387(T)), P. cepalis sp. nov. (type strain LMG 31106(T) = CCUG 39680(T)), P. commovens sp. nov. (type strain LMG 31010(T) = CCUG 73378(T)), P. communis sp. nov. (type strain LMG 31110(T) = CCUG 73383(T)), P. eparura sp. nov. (type strain LMG 31012(T) = CCUG 73380(T)), P. horticolens sp. nov. (type strain LMG 31112(T) = CCUG 73379(T)), P. iniqua sp. nov. (type strain LMG 31009(T) = CCUG 73377(T)), P. morbifera sp. nov. (type strain LMG 31116(T) = CCUG 73389(T)), P. nosoerga sp. nov. (type strain LMG 31109(T) = CCUG 73390(T)), P. pneumonica sp. nov. (type strain LMG 31114(T) = CCUG 73388(T)), P. soli sp. nov. (type strain LMG 31014(T) = CCUG 73382(T)), and P. terrigena sp. nov. (type strain LMG 31013(T) = CCUG 73381(T)).
Keywords
Pandoraea, novel species, cystic fibrosis microbiology, comparative genomics, xenobiotics, biodegradation, opportunistic pathogens, CYSTIC-FIBROSIS PATIENT, SP NOV., EPIDEMIC SPREAD, SPUTORUM, DEGRADATION, ANNOTATION, APISTA, TOOL, IDENTIFICATION, RHIZOSPHERE

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MLA
Peeters, Charlotte, et al. “Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism.” FRONTIERS IN MICROBIOLOGY, vol. 10, 2019.
APA
Peeters, C., De Canck, E., Cnockaert, M., De Brandt, E., Snauwaert, C., Verheyde, B., … Vandamme, P. (2019). Comparative genomics of Pandoraea, a genus enriched in xenobiotic biodegradation and metabolism. FRONTIERS IN MICROBIOLOGY, 10.
Chicago author-date
Peeters, Charlotte, Evelien De Canck, Margo Cnockaert, Evie De Brandt, Cindy Snauwaert, Bart Verheyde, Eliza Depoorter, Theodore Spilker, John J LiPuma, and Peter Vandamme. 2019. “Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism.” FRONTIERS IN MICROBIOLOGY 10.
Chicago author-date (all authors)
Peeters, Charlotte, Evelien De Canck, Margo Cnockaert, Evie De Brandt, Cindy Snauwaert, Bart Verheyde, Eliza Depoorter, Theodore Spilker, John J LiPuma, and Peter Vandamme. 2019. “Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism.” FRONTIERS IN MICROBIOLOGY 10.
Vancouver
1.
Peeters C, De Canck E, Cnockaert M, De Brandt E, Snauwaert C, Verheyde B, et al. Comparative genomics of Pandoraea, a genus enriched in xenobiotic biodegradation and metabolism. FRONTIERS IN MICROBIOLOGY. 2019;10.
IEEE
[1]
C. Peeters et al., “Comparative genomics of Pandoraea, a genus enriched in xenobiotic biodegradation and metabolism,” FRONTIERS IN MICROBIOLOGY, vol. 10, 2019.
@article{8636961,
  abstract     = {Comparative analysis of partial gyrB, recA, and gltB gene sequences of 84 Pandoraea reference strains and field isolates revealed several clusters that included no taxonomic reference strains. The gyrB, recA, and gltB 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 Pandoraea 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 Pandoraea species among the strains analyzed, and allowed the identification of several unclassified Pandoraea strains reported in the literature. The genus Pandoraea 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 Pandoraea species as P. anapnoica sp. nov. (type strain LMG 31117(T) = CCUG 73385(T)), P. anhela sp. nov. (type strain LMG 31108(T) = CCUG 73386(T)), P. aquatica sp. nov. (type strain LMG 31011(T) = CCUG 73384(T)), P. bronchicola sp. nov. (type strain LMG 20603(T) = ATCC BAA-110(T)), P. capi sp. nov. (type strain LMG 20602(T) = ATCC BAA-109(T)), P. captiosa sp. nov. (type strain LMG 31118(T) = CCUG 73387(T)), P. cepalis sp. nov. (type strain LMG 31106(T) = CCUG 39680(T)), P. commovens sp. nov. (type strain LMG 31010(T) = CCUG 73378(T)), P. communis sp. nov. (type strain LMG 31110(T) = CCUG 73383(T)), P. eparura sp. nov. (type strain LMG 31012(T) = CCUG 73380(T)), P. horticolens sp. nov. (type strain LMG 31112(T) = CCUG 73379(T)), P. iniqua sp. nov. (type strain LMG 31009(T) = CCUG 73377(T)), P. morbifera sp. nov. (type strain LMG 31116(T) = CCUG 73389(T)), P. nosoerga sp. nov. (type strain LMG 31109(T) = CCUG 73390(T)), P. pneumonica sp. nov. (type strain LMG 31114(T) = CCUG 73388(T)), P. soli sp. nov. (type strain LMG 31014(T) = CCUG 73382(T)), and P. terrigena sp. nov. (type strain LMG 31013(T) = CCUG 73381(T)).},
  articleno    = {2556},
  author       = {Peeters, Charlotte and De Canck, Evelien and Cnockaert, Margo and De Brandt, Evie and Snauwaert, Cindy and Verheyde, Bart and Depoorter, Eliza and Spilker, Theodore and LiPuma, John J and Vandamme, Peter},
  issn         = {1664-302X},
  journal      = {FRONTIERS IN MICROBIOLOGY},
  keywords     = {Pandoraea,novel species,cystic fibrosis microbiology,comparative genomics,xenobiotics,biodegradation,opportunistic pathogens,CYSTIC-FIBROSIS PATIENT,SP NOV.,EPIDEMIC SPREAD,SPUTORUM,DEGRADATION,ANNOTATION,APISTA,TOOL,IDENTIFICATION,RHIZOSPHERE},
  language     = {eng},
  pages        = {21},
  title        = {Comparative genomics of Pandoraea, a genus enriched in xenobiotic biodegradation and metabolism},
  url          = {http://dx.doi.org/10.3389/fmicb.2019.02556},
  volume       = {10},
  year         = {2019},
}

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