The Ever-Expanding <i>Pseudomonas</i> Genus: Description of 43 New Species and Partition of the <i>Pseudomonas putida</i> Group
The genus <i>Pseudomonas</i> hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of <i>Pseudomonas</i> are well known to represent only a small fraction of this diversity and the number of available <i>Pseudom...
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MDPI AG
2021-08-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/8/1766 |
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| author | Léa Girard Cédric Lood Monica Höfte Peter Vandamme Hassan Rokni-Zadeh Vera van Noort Rob Lavigne René De Mot |
| author_facet | Léa Girard Cédric Lood Monica Höfte Peter Vandamme Hassan Rokni-Zadeh Vera van Noort Rob Lavigne René De Mot |
| author_sort | Léa Girard |
| collection | DOAJ |
| description | The genus <i>Pseudomonas</i> hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of <i>Pseudomonas</i> are well known to represent only a small fraction of this diversity and the number of available <i>Pseudomonas</i> genome sequences is increasing rapidly. Consequently, new <i>Pseudomonas</i> 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 <i>Pseudomonas</i> species and provide an update of the <i>Pseudomonas</i> evolutionary and taxonomic relationships. Phylogenies based on the <i>rpoD</i> gene and whole genome sequences, including, respectively, 316 and 313 type strains of <i>Pseudomonas</i>, revealed sixteen groups of <i>Pseudomonas</i> and, together with the distribution of cyclic lipopeptide biosynthesis gene clusters, enabled the partitioning of the <i>P. putida</i> group into fifteen subgroups. Pairwise average nucleotide identities were calculated between type strains and a selection of 60 genomes of non-type strains of <i>Pseudomonas</i>. Forty-one strains were incorrectly assigned at the species level and among these, 19 strains were shown to represent an additional 13 new <i>Pseudomonas</i> 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 <i>Pseudomonas</i> spp. |
| first_indexed | 2024-03-10T08:34:19Z |
| format | Article |
| id | doaj.art-882d572105a24bcd8febb82b09a21332 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T08:34:19Z |
| publishDate | 2021-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-882d572105a24bcd8febb82b09a213322023-11-22T08:48:33ZengMDPI AGMicroorganisms2076-26072021-08-0198176610.3390/microorganisms9081766The Ever-Expanding <i>Pseudomonas</i> Genus: Description of 43 New Species and Partition of the <i>Pseudomonas putida</i> GroupLéa Girard0Cédric Lood1Monica Höfte2Peter Vandamme3Hassan Rokni-Zadeh4Vera van Noort5Rob Lavigne6René De Mot7Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, BelgiumCentre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, BelgiumDepartment of Plants and Crops, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Ghent, BelgiumLaboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, BelgiumZanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, Zanjan 45139-56184, IranCentre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, BelgiumDepartment of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, BelgiumCentre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, BelgiumThe genus <i>Pseudomonas</i> hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of <i>Pseudomonas</i> are well known to represent only a small fraction of this diversity and the number of available <i>Pseudomonas</i> genome sequences is increasing rapidly. Consequently, new <i>Pseudomonas</i> 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 <i>Pseudomonas</i> species and provide an update of the <i>Pseudomonas</i> evolutionary and taxonomic relationships. Phylogenies based on the <i>rpoD</i> gene and whole genome sequences, including, respectively, 316 and 313 type strains of <i>Pseudomonas</i>, revealed sixteen groups of <i>Pseudomonas</i> and, together with the distribution of cyclic lipopeptide biosynthesis gene clusters, enabled the partitioning of the <i>P. putida</i> group into fifteen subgroups. Pairwise average nucleotide identities were calculated between type strains and a selection of 60 genomes of non-type strains of <i>Pseudomonas</i>. Forty-one strains were incorrectly assigned at the species level and among these, 19 strains were shown to represent an additional 13 new <i>Pseudomonas</i> 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 <i>Pseudomonas</i> spp.https://www.mdpi.com/2076-2607/9/8/1766Pseudomonadaceaelong-read sequencinghybrid assemblytaxonomyphylogenyNon-Ribosomal Peptide Synthetase (NRPS) |
| spellingShingle | Léa Girard Cédric Lood Monica Höfte Peter Vandamme Hassan Rokni-Zadeh Vera van Noort Rob Lavigne René De Mot The Ever-Expanding <i>Pseudomonas</i> Genus: Description of 43 New Species and Partition of the <i>Pseudomonas putida</i> Group Microorganisms Pseudomonadaceae long-read sequencing hybrid assembly taxonomy phylogeny Non-Ribosomal Peptide Synthetase (NRPS) |
| title | The Ever-Expanding <i>Pseudomonas</i> Genus: Description of 43 New Species and Partition of the <i>Pseudomonas putida</i> Group |
| title_full | The Ever-Expanding <i>Pseudomonas</i> Genus: Description of 43 New Species and Partition of the <i>Pseudomonas putida</i> Group |
| title_fullStr | The Ever-Expanding <i>Pseudomonas</i> Genus: Description of 43 New Species and Partition of the <i>Pseudomonas putida</i> Group |
| title_full_unstemmed | The Ever-Expanding <i>Pseudomonas</i> Genus: Description of 43 New Species and Partition of the <i>Pseudomonas putida</i> Group |
| title_short | The Ever-Expanding <i>Pseudomonas</i> Genus: Description of 43 New Species and Partition of the <i>Pseudomonas putida</i> Group |
| title_sort | ever expanding i pseudomonas i genus description of 43 new species and partition of the i pseudomonas putida i group |
| topic | Pseudomonadaceae long-read sequencing hybrid assembly taxonomy phylogeny Non-Ribosomal Peptide Synthetase (NRPS) |
| url | https://www.mdpi.com/2076-2607/9/8/1766 |
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