Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene

Microorganisms

Cédric Lood¹  René De Mot¹  Vera van Noort¹  Léa Girard¹  Rob Lavigne²  Hassan Rokni-Zadeh³ 

[1] Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium;Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium;Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, 45139-56184 Zanjan, Iran;

关键词: species identification;    taxonomy;    phylogeny;    diversity;    genome sequencing;   

DOI  :  10.3390/microorganisms8081166

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown