Re-identification of strains deposited as Pseudomonas aeruginosa, Pseudomonas fluorescens and Pseudomonas putida in GenBank based on whole genome sequences.

The taxonomic classification of Pseudomonas species has been revised and updated several times. This study utilized average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) cutoff values of 95 and 70 %, respectively, to re-identify the species of strains deposited in GenBank as P. aeruginosa, P. fluorescens and P. putida. Of the 264 deposited P. aeruginosa strains, 259 were correctly identified as P. aeruginosa, but the remaining five were not. All 28 deposited P. fluorescens strains had been incorrectly identified as P. fluorescens. Four of these strains were re-identified, including two as P. kilonensis and one each as P. aeruginosa and P. brassicacearum, but the remaining 24 could not be re-identified. Similarly, all 35 deposited P. putida strains had been incorrectly identified as P. putida. Nineteen of these strains were re-identified, including 12 as P. alloputida, four as P. asiatica and one each as P. juntendi, P. monteilii and P. mosselii. These results strongly suggest that Pseudomonas bacteria should be identified using ANI and dDDH analyses based on whole genome sequencing when Pseudomonas species are initially deposited in GenBank/DDBJ/EMBL databases.

Citation

Yuh Morimoto, Mari Tohya, Zulipiya Aibibula, Tadashi Baba, Hiroyuki Daida, Teruo Kirikae. Re-identification of strains deposited as Pseudomonas aeruginosa, Pseudomonas fluorescens and Pseudomonas putida in GenBank based on whole genome sequences. International journal of systematic and evolutionary microbiology. 2020 Nov;70(11):5958-5963

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PMID: 32936751

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