Phylogenomic and comparative genomic studies robustly demarcate two distinct clades of Pseudomonas aeruginosa strains: proposal to transfer the strains from an outlier clade to a novel species Pseudomonas paraeruginosa sp. nov.

Abstract

The strains of Pseudomonas aeruginosa exhibit considerable differences in their genotypic and pathogenic properties. To clarify their evolutionary/taxonomic relationships, comprehensive phylogenomic and comparative genomic studies were conducted on the genome sequences of 212 P . aeruginosa strains covering their genetic diversity. In a phylogenomic tree based on 118 conserved proteins, the analysed strains formed two distinct clades. One of these clades, Clade-1, encompassing >70 % of the strains including the type strain DSM 50071T, represents the species P. aeruginosa sensu stricto. Clade-2, referred to in earlier work as the outlier group, with NCTC 13628T as its type strain, constitutes a novel species level lineage. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the strains from Clade-1 and Clade-2 are in the range of 93.4–93.7, 95.1–95.3 and 52–53 %, respectively. The 16S rRNA gene of P. aeruginosa DSM 50071T also shows 98.3 % similarity to that of NCTC 13628T. These values are lower than the suggested cut-off values for species distinction, indicating that the Clade-2 strains (NCTC 13628T) constitute a new species. We also report the identification of 12 conserved signature indels in different proteins and 24 conserved signature proteins that are exclusively found in either Clade-1 or Clade-2, providing a reliable means for distinguishing these clades. Additionally, in contrast to swimming motility, twitching motility is only present in Clade-1 strains. Based on earlier work, the strains from these two clades also differ in their pathogenic mechanisms (presence/absence of Type III secretion system), production of biosurfactants, phenazines and siderophores, and several other genomic characteristics. Based on the evidence from different studies, we propose that the Clade-2 strains constitute a novel species for which the name Pseudomonas paraeruginosa is proposed. The type strain is NCTC 13628T (=PA7T=ATCC 9027T). The description of Pseudomonas aeruginosa is also emended to include information for different molecular markers specific for this species.

AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species

“…Different CSIs which are part of our database were all considered specific or useful for the identification of indicated taxa in our published work [36, 52, 58, 64, 66, 75–77, 79, 80]. However, in these studies, the taxa specificities of the CSIs were generally assessed by examining the top 300–500 blast p hits [48, 52, 58, 64, 75].…”

“…aeruginosa and P. paraeruginosa [79]. These two closely related species cannot be easily distinguished based on the 16S rRNA or other single gene(s) trees [79]. However, multiple CSIs specific for these two species have been identified and they are present in the server database [79].…”

“…These two closely related species cannot be easily distinguished based on the 16S rRNA or other single gene(s) trees [79]. However, multiple CSIs specific for these two species have been identified and they are present in the server database [79]. Based upon them, the server can reliably distinguish the strains belonging to the two species.…”

“…Recently, the available strains of Pseudomonas aeruginosa were divided into two separate species, P. aeruginosa and P. paraeruginosa [79]. These two closely related species cannot be easily distinguished based on the 16S rRNA or other single gene(s) trees [79].…”

“…Of these, >210 CSIs are specific for >30 Bacillaceae genera into which species from the genus Bacillus were recently reclassified [52, 58, 66], whereas 138 CSIs are specific for the families Caryophanaceae and Leuconostocaceae and multiple genera and clades within them [66, 75]. In addition, our database also includes information for >230 CSIs that are specific for members of several other prokaryotic taxa including members of the order Legionellales [64], Neisseriales [76], Chlorobiales [77], family Borreliaceae [36, 53, 78], as well as some species/genera belonging to the family Pseudomonadaceae [79, 80]. Presently, our database includes CSIs for only those clades/taxa whose specificities was examined within the past 2 years [36, 53, 64, 76–78, 81].…”