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Indian J Microbiol. 2013 Sep;53(3):253-63. doi: 10.1007/s12088-013-0412-1. Epub 2013 Apr 23.

Development of Genomic Tools for the Identification of Certain Pseudomonas up to Species Level.

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  • 1Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India.
  • 2Environmental Genomics Unit, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020 India.


Pseudomonas is a highly versatile bacterium at the species level with great ecological significance. These genetically and metabolically diverse species have undergone repeated taxonomic revisions. We propose a strategy to identify Pseudomonas up to species level, based on the unique features of their 16S rDNA (rrs) gene sequence, such as the frame work of sequences, sequence motifs and restriction endonuclease (RE) digestion patterns. A species specific phylogenetic framework composed of 31 different rrs sequences, allowed us to segregate 1,367 out of 2,985 rrs sequences of this genus, which have been classified at present only up to genus (Pseudomonas) level, as follows: P. aeruginosa (219 sequences), P. fluorescens (463 sequences), P. putida (347 sequences), P. stutzeri (197 sequences), and P. syringae (141 sequences). These segregations were validated by unique 30-50 nucleotide long motifs and RE digestion patterns in their rrs. A single gene thus provides multiple makers for identification and surveillance of Pseudomonas.


Diversity; Evolution; Framework; Phylogeny; Pseudomonas; Restriction endonuclease

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