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 31117T = CCUG 73385T), P. anhela sp. nov. (type strain LMG 31108T = CCUG 73386T), P. aquatica sp. nov. (type strain LMG 31011T = CCUG 73384T), P. bronchicola sp. nov. (type strain LMG 20603T = ATCC BAA-110T), P. capi sp. nov. (type strain LMG 20602T = ATCC BAA-109T), P. captiosa sp. nov. (type strain LMG 31118T = CCUG 73387T), P. cepalis sp. nov. (type strain LMG 31106T = CCUG 39680T), P. commovens sp. nov. (type strain LMG 31010T = CCUG 73378T), P. communis sp. nov. (type strain LMG 31110T = CCUG 73383T), P. eparura sp. nov. (type strain LMG 31012T = CCUG 73380T), P. horticolens sp. nov. (type strain LMG 31112T = CCUG 73379T), P. iniqua sp. nov. (type strain LMG 31009T = CCUG 73377T), P. morbifera sp. nov. (type strain LMG 31116T = CCUG 73389T), P. nosoerga sp. nov. (type strain LMG 31109T = CCUG 73390T), P. pneumonica sp. nov. (type strain LMG 31114T = CCUG 73388T), P. soli sp. nov. (type strain LMG 31014T = CCUG 73382T), and P. terrigena sp. nov. (type strain LMG 31013T = CCUG 73381T).
Highlights
IntroductionMembers of the genus Pandoraea have emerged as rare opportunistic pathogens in persons with cystic fibrosis (Jørgensen et al, 2003; Johnson et al, 2004; Pimentel and MacLeod, 2008; Kokcha et al, 2013; Ambrose et al, 2016; Martina et al, 2017; See-Too et al, 2019) and several cases of chronic colonization and patient-to-patient transfer in this patient group have been reported (Jørgensen et al, 2003; Atkinson et al, 2006; Degand et al, 2015; Pugès et al, 2015; Ambrose et al, 2016; Dupont et al, 2017; Greninger et al, 2017)
The latter suggests they may be important contributors to soil formation, soil fertility and retention, and cycling of elements necessary for plant growth (Sahin, 2003). These freeliving Pandoraea bacteria are often enriched in polluted soils and participate in the biodegradation of complex organic substances including lignin (Shi et al, 2013; Kumar et al, 2018b; Liu et al, 2019), biodiesel and petroleum by-products, p-xylene (Wang et al, 2015), δ-hexachlorocyclohexane (Pushiri et al, 2013), din-butyl phthalate (Yang et al, 2018), biphenyl, benzoate and naphthalene (Uhlik et al, 2012), and tetracycline (Wu et al, 2019) and β-lactam antibiotics (Crofts et al, 2017)
Because many Pandoraea strains participate in the biodegradation of recalcitrant xenobiotics (Uhlik et al, 2012; Pushiri et al, 2013; Shi et al, 2013; Wang et al, 2015; Crofts et al, 2017; de Paula et al, 2017; Sarkar et al, 2017; Tirado-Torres et al, 2017; Kumar et al, 2018b; Yang et al, 2018; Liu et al, 2019; Wu et al, 2019), we looked at the orthogroups in the kyoto encyclopedia of genes and genomes (KEGG) pathway Xenobiotics biodegradation and metabolism (Figure 7)
Summary
Members of the genus Pandoraea have emerged as rare opportunistic pathogens in persons with cystic fibrosis (Jørgensen et al, 2003; Johnson et al, 2004; Pimentel and MacLeod, 2008; Kokcha et al, 2013; Ambrose et al, 2016; Martina et al, 2017; See-Too et al, 2019) and several cases of chronic colonization and patient-to-patient transfer in this patient group have been reported (Jørgensen et al, 2003; Atkinson et al, 2006; Degand et al, 2015; Pugès et al, 2015; Ambrose et al, 2016; Dupont et al, 2017; Greninger et al, 2017). A growing number of reports demonstrate that soil and water represent the natural habitats of Pandoraea bacteria where they can be part of rhizosphere communities (Anandham et al, 2010; Jurelevicius et al, 2010; Peeters et al, 2016; Dong et al, 2018) and be involved in oxalate degradation (Jin et al, 2007; Sahin et al, 2011) The latter suggests they may be important contributors to soil formation, soil fertility and retention, and cycling of elements necessary for plant growth (Sahin, 2003). This strain represented a separate novel Pandoraea species, it was not formally classified (Coenye et al, 2000) pending the availability of more than one strain representing the same novel species, a taxonomic practice that has been largely abandoned today
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