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Phylogeny and genomic analysis of Shewanella cutis sp. nov., isolated from freshwater pufferfish
L. Das, RRA. Kujur, T. Debnath, SK. Das
Language English Country Czech Republic
Document type Journal Article
Grant support
D.O.No. BT/PR7661/AAQ/3/629/2013
Department of Biotechnology, Ministry of Science and Technology, India
- MeSH
- DNA, Bacterial * genetics MeSH
- Phospholipids analysis MeSH
- Phylogeny * MeSH
- Genome, Bacterial * MeSH
- Genomics MeSH
- Skin microbiology MeSH
- Fatty Acids * analysis MeSH
- RNA, Ribosomal, 16S * genetics MeSH
- Sequence Analysis, DNA MeSH
- Shewanella * genetics isolation & purification classification MeSH
- Fresh Water microbiology MeSH
- Bacterial Typing Techniques MeSH
- Tetraodontiformes * microbiology MeSH
- Base Composition * MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
Three closely related, aerobic, Gram-stain-negative, motile, rod-shaped bacterial strains (PS-2T, PS-17, and PS-19) were isolated from the skin of freshwater pufferfish (Tetraodon cutcutia). Colonies are pinkish-colored. The optimum growth occurred at 28-30 °C, and the pH was 6.5-7. The major cellular fatty acids were C16:1 ω7c, iso-C15.0, C17:1 ω8c, C18:1 ω7c, and C16:0. The predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and amino lipids. The genome size of strain PS-2T is 4.8 Mbp, and the G + C content was 46.0%. The major fraction of genes were associated with biological processes (45.64%), followed by molecular function (29.86%) and cellular components (24.49%). The unique genes identified in strain PS-2T secreted cyanophycinase, UDP-N-acetylglucosamine 2-epimerase, methyltransferase, kynureninase, ADA regulatory protein, biphenyl degradation, thermostable carboxypeptidase 1, tetrathionate respiration, etc. In addition, alanine and glutamate racemases were present. The 16S rRNA gene sequences shared 98.83-99.24% similarity with the closely related type strains of Shewanella. The ANI and AAI of strain PS-2T with reference type strains of the genus Shewanella were below 95-96%, and the corresponding dDDH values were below 70%. A phylogenetic tree based on 16S rRNA gene sequences and genome-wide core genes revealed that strain PS-2T clustered with Shewanella oneidensis LMG 19005T in both phylogenetic trees. Based on the polyphasic analysis, the new isolates (PS-2T, PS-17, and PS-19) represent a novel species of Shewanella, for which Shewanella cutis sp. nov. is proposed. The type strain is PS-2T (= TBRC 15838T = NBRC 115342T).
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