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
Article
Rudra, B., Duncan, L., Shah, A., Shah, H. and Gupta, R. 2022. 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. International Journal of Systematic and Evolutionary Microbiology. 72 (11), pp. 1-15. https://doi.org/10.1099/ijsem.0.005542
Type | Article |
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Title | 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 |
Authors | Rudra, B., Duncan, L., Shah, A., Shah, H. and Gupta, R. |
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 NCTC13628T. 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. |
Keywords | classical clade, conserved signature indels (CSIs), conserved signature proteins (CSPs), outlier clade, Pseudomonas aeruginosa, Pseudomonas paraeruginosa, systematics, T3SS system |
Sustainable Development Goals | 3 Good health and well-being |
Middlesex University Theme | Health & Wellbeing |
Publisher | Microbiology Society |
Journal | International Journal of Systematic and Evolutionary Microbiology |
ISSN | 1466-5026 |
Electronic | 1466-5034 |
Publication dates | |
Online | 09 Nov 2022 |
10 Nov 2022 | |
Publication process dates | |
Deposited | 06 Oct 2022 |
Submitted | 03 May 2022 |
Accepted | 19 Jul 2022 |
Output status | Published |
Publisher's version | License |
Copyright Statement | © 2022 The Authors |
Additional information | Correction publlished: Rudra, B., Duncan, L., Shah, A. J., Shah, H. N., & Gupta, R. S. (2023). Corrigendum: 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. International Journal of Systematic and Evolutionary Microbiology, 73(3). https://doi.org/10.1099/ijsem.0.005828 |
Digital Object Identifier (DOI) | https://doi.org/10.1099/ijsem.0.005542 |
Related Output | |
Is supplemented by | https://doi.org/10.1099/ijsem.0.005828 |
Language | English |
File | License |
https://repository.mdx.ac.uk/item/8q133
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