The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group

The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Co...

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Vydáno v:Microorganisms (Basel) Ročník 9; číslo 8; s. 1766
Hlavní autoři: Girard, Léa, Lood, Cédric, Höfte, Monica, Vandamme, Peter, Rokni-Zadeh, Hassan, van Noort, Vera, Lavigne, Rob, De Mot, René
Médium: Journal Article
Jazyk:angličtina
Vydáno: Basel MDPI AG 18.08.2021
MDPI
Témata:
Bacteria
Biosynthesis
Evolution
Gene clusters
Gene sequencing
Genera
Genetic diversity
genetic variation
Genomes
Gram-negative bacteria
hybrid assembly
Hybridization
lifestyle
lipopeptides
long-read sequencing
Metabolites
New species
Non-Ribosomal Peptide Synthetase (NRPS)
Nucleotides
Phylogenetics
Phylogeny
Pseudomonadaceae
Pseudomonas
Pseudomonas putida
RpoD gene
Strains (organisms)
Subgroups
Taxonomy
Whole genome sequencing
ISSN:2076-2607, 2076-2607
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Shrnutí:The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Consequently, new Pseudomonas species are regularly reported and the number of species within the genus is constantly evolving. In this study, whole genome sequencing enabled us to define 43 new Pseudomonas species and provide an update of the Pseudomonas evolutionary and taxonomic relationships. Phylogenies based on the rpoD gene and whole genome sequences, including, respectively, 316 and 313 type strains of Pseudomonas, revealed sixteen groups of Pseudomonas and, together with the distribution of cyclic lipopeptide biosynthesis gene clusters, enabled the partitioning of the P. putida group into fifteen subgroups. Pairwise average nucleotide identities were calculated between type strains and a selection of 60 genomes of non-type strains of Pseudomonas. Forty-one strains were incorrectly assigned at the species level and among these, 19 strains were shown to represent an additional 13 new Pseudomonas species that remain to be formally classified. This work pinpoints the importance of correct taxonomic assignment and phylogenetic classification in order to perform integrative studies linking genetic diversity, lifestyle, and metabolic potential of Pseudomonas spp.
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The authors contributed equally to this work.
ISSN:2076-2607
2076-2607
DOI:10.3390/microorganisms9081766