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Article

Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene

1
Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
2
Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
3
Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, 45139-56184 Zanjan, Iran
4
Institute of Biology, Leiden University, Sylviusweg 72, 2333 Leiden, The Netherlands
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(8), 1166; https://doi.org/10.3390/microorganisms8081166
Received: 23 June 2020 / Revised: 27 July 2020 / Accepted: 28 July 2020 / Published: 31 July 2020
(This article belongs to the Special Issue Microbial Isolation and Characterization)
The taxonomic affiliation of Pseudomonas isolates is currently assessed by using the 16S rRNA gene, MultiLocus Sequence Analysis (MLSA), or whole genome sequencing. Therefore, microbiologists are facing an arduous choice, either using the universal marker, knowing that these affiliations could be inaccurate, or engaging in more laborious and costly approaches. The rpoD gene, like the 16S rRNA gene, is included in most MLSA procedures and has already been suggested for the rapid identification of certain groups of Pseudomonas. However, a comprehensive overview of the rpoD-based phylogenetic relationships within the Pseudomonas genus is lacking. In this study, we present the rpoD-based phylogeny of 217 type strains of Pseudomonas and defined a cutoff value of 98% nucleotide identity to differentiate strains at the species level. To validate this approach, we sequenced the rpoD of 145 environmental isolates and complemented this analysis with whole genome sequencing. The rpoD sequence allowed us to accurately assign Pseudomonas isolates to 20 known species and represents an excellent first diagnostic tool to identify new Pseudomonas species. Finally, rpoD amplicon sequencing appears as a reliable and low-cost alternative, particularly in the case of large environmental studies with hundreds or thousands of isolates. View Full-Text
Keywords: species identification; taxonomy; phylogeny; diversity; genome sequencing species identification; taxonomy; phylogeny; diversity; genome sequencing
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MDPI and ACS Style

Girard, L.; Lood, C.; Rokni-Zadeh, H.; van Noort, V.; Lavigne, R.; De Mot, R. Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene. Microorganisms 2020, 8, 1166. https://doi.org/10.3390/microorganisms8081166

AMA Style

Girard L, Lood C, Rokni-Zadeh H, van Noort V, Lavigne R, De Mot R. Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene. Microorganisms. 2020; 8(8):1166. https://doi.org/10.3390/microorganisms8081166

Chicago/Turabian Style

Girard, Léa, Cédric Lood, Hassan Rokni-Zadeh, Vera van Noort, Rob Lavigne, and René De Mot. 2020. "Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene" Microorganisms 8, no. 8: 1166. https://doi.org/10.3390/microorganisms8081166

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