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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 ).

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