Phylogeny and genomic analysis of Shewanella cutis sp. nov., isolated from freshwater pufferfish
Jazyk angličtina Země Spojené státy americké Médium print-electronic
Typ dokumentu časopisecké články
Grantová podpora
D.O.No. BT/PR7661/AAQ/3/629/2013
Department of Biotechnology, Ministry of Science and Technology, India
PubMed
37996658
DOI
10.1007/s12223-023-01111-6
PII: 10.1007/s12223-023-01111-6
Knihovny.cz E-zdroje
- Klíčová slova
- Shewanella cutis sp. nov, Genome analysis, Phylogenetic analysis, Pufferfish,
- MeSH
- DNA bakterií * genetika MeSH
- fosfolipidy analýza MeSH
- fylogeneze * MeSH
- genom bakteriální * MeSH
- genomika MeSH
- kůže mikrobiologie MeSH
- mastné kyseliny * analýza MeSH
- RNA ribozomální 16S * genetika MeSH
- sekvenční analýza DNA MeSH
- Shewanella * genetika izolace a purifikace klasifikace MeSH
- sladká voda mikrobiologie MeSH
- techniky typizace bakterií MeSH
- Tetraodontiformes * mikrobiologie MeSH
- zastoupení bazí * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DNA bakterií * MeSH
- fosfolipidy MeSH
- mastné kyseliny * MeSH
- RNA ribozomální 16S * 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).
Zobrazit více v PubMed
Bernardet JF, Nakagawa Y, Holmes B, Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070. https://doi.org/10.1099/00207713-52-3-1049
Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917. https://doi.org/10.1139/o59-099 PubMed DOI
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170 PubMed DOI PMC
Brink AJ, van Straten A, van Rensburg AJ (1995) Shewanella (Pseudomonas) putrefaciens bacteremia. Clin Infect Dis 20:1327–1332. https://doi.org/10.1093/clinids/20.5.1327 PubMed DOI
Das L, Deb S, Arakawa E, Yamasaki S, Das SK (2022) Pufferfish (Tetraodon cutcutia) sampled from a freshwater river serves as an intermediate reservoir of a sucrose nonfermenting variant of Vibrio cholerae PS-4. Microbiol Spectr 10:e01221–e1321. https://doi.org/10.1128/spectrum.01221-21
Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. https://doi.org/10.1093/bioinformatics/btt086 PubMed DOI PMC
Hernández SB, Cava F (2016) Environmental roles of microbial amino acid racemases. Environ Microbiol 18:1673–1685. https://doi.org/10.1111/1462-2920.13072 PubMed DOI
Hirota K, Nodasaka Y, Orikasa Y, Okuyama H, Yumoto I (2005) Shewanella pneumatophori sp. nov., an eicosapentaenoic acid-producing marine bacterium isolated from the intestines of Pacific mackerel (Pneumatophorus japonicus). Int J Syst Evol Microbiol 55:2355–2359. https://doi.org/10.1099/ijs.0.63804-0 PubMed DOI
Huang J, Sun B, Zhang X (2010) Shewanella xiamenensis sp. nov., isolated from coastal sea sediment. Int J Syst Evol Microbiol 60:1585–1589. https://doi.org/10.1099/ijs.0.013300-0 PubMed DOI
Ivanova EP, Flavier S, Christen R (2004) Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int J Syst Evol Microbiol 54:1773–1788. https://doi.org/10.1099/ijs.0.02997-0 PubMed DOI
Jiang J, Pan Y, Hu S, Zhang X, Hu B, Huang H, Hong S, Meng J, Li C, Wang K (2014) Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils. Int J Syst Evol Microbiol 64:1662–1669. https://doi.org/10.1099/ijs.0.056499-0 PubMed DOI
Jorgensen BR, Huß HH (1989) Growth and activity of Shewanella putrefaciens isolated from spoiling fish. Int J Food Microbiol 9:51–62. https://doi.org/10.1016/0168-1605(89)90037-8 PubMed DOI
Jung YT, Oh TK, Yoon JH (2012) Marinomonas hwangdonensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 62:2062–2067. https://doi.org/10.1099/ijs.0.036582-0 PubMed DOI
Jyoti V, Narayan KD, Das SK (2010) Gulbenkiania indica sp. nov. isolated from a sulfur spring. Int J Syst Evol Microbiol 60:1052–1055. https://doi.org/10.1099/ijs.0.014035-0
Kim D, Baik KS, Kim MS, Jung BM, Shin TS, Chung GH, Rhee MS, Seong CN (2007) Shewanella haliotis sp. nov., isolated from the gut microflora of abalone, Haliotis discus hannai. Int J Syst Evol Microbiol 57:2926–2931. https://doi.org/10.1099/ijs.0.65257-0 PubMed DOI
Kim KK, Kim YO, Park S, Kang SJ, Nam BH, Kim DN, Oh TK, Yoon JH (2011) Shewanella upenei sp. nov., a lipolytic bacterium isolated from bensasi goatfish Upeneus bensasi. J Microbiol 49:381–386. https://doi.org/10.1007/s12275-011-0175-5 PubMed DOI
Konstantinidis KT, Tiedje JM (2005a) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2572. https://doi.org/10.1073/pnas.0409727102 PubMed DOI PMC
Konstantinidis KT, Tiedje JM (2005b) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 87:6258–6264. https://doi.org/10.1128/JB.187.18.6258-6264.2005 DOI
Kumari P, Poddar A, Das SK (2014) Marinomonas fungiae sp. nov., isolated from the coral Fungia echinata from the Andaman Sea. Int J Syst Evol Microbiol 64:487–494. https://doi.org/10.1099/ijs.0.054809-0 PubMed DOI
Lee OO, Lau SCK, Tsoi MMY, Li X, Plakhotnikova I, Dobretsov S, Wu MCS, Wong PK, Weinbauer M, Qian PY (2006) Shewanella irciniae sp. nov., a novel member of the family Shewanellaceae, isolated from the marine sponge Ircinia dendroides in the Bay of Villefranche, Mediterranean Sea. Int J Syst Evol Microbiol 56:2871–2877. https://doi.org/10.1099/ijs.0.64562-0 PubMed DOI
Liu Y, Shang XX, Yi ZW, Gu L, Zeng RY (2015) Shewanella mangrovi sp. nov., an acetaldehyde-degrading bacterium isolated from mangrove sediment. Int J Syst Evol Microbiol 65:2630–2634. https://doi.org/10.1099/ijs.0.000313 PubMed DOI
MacDonell MT, Colwell RR (1985) Phylogeny of the Vibrionaceae, and recommendation for two new genera, Listonella and Shewanella. Syst Appl Microbiol 6:171–182. https://doi.org/10.1016/S0723-2020(85)80051-5 DOI
Martín-Rodríguez AJ, Meier-Kolthoff JP (2022) Whole genome-based taxonomy of Shewanella and Parashewanella. Int J Syst Evol Microbiol 72:005438. https://doi.org/10.1099/ijsem.0.005438 DOI
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. http://www.biomedcentral.com/1471-2105/14/60
Myers CR, Nealson KH (1988) Manganese reduction bacteria and growth with manganese oxide as the sole electron acceptor. Science 240:1319–1321. https://doi.org/10.1126/science.240.4857.1319 PubMed DOI
Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I, Chun J (2018) UBCG: up-todate bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285. https://doi.org/10.1007/s12275-018-8014-6 PubMed DOI
Narayan KD, Pandey SK, Das SK (2010) Characterization of Comamonas thiooxidans sp. nov., and comparison of thiosulfate oxidation with Comamonas testosterone and Comamonas composti. Curr Microbiol 61:248–253. https://doi.org/10.1007/s00284-010-9602-9 PubMed DOI
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214. https://doi.org/10.1093/nar/gkt1226 PubMed DOI
Park HY, Jeon CO (2013) Shewanella aestuarii sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 63:4683–4690. https://doi.org/10.1099/ijs.0.055178-0 PubMed DOI
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. https://doi.org/10.1101/gr.186072.114 PubMed DOI PMC
Petrovskis EA, Vogel TM, Adriaens P (1994) Effects of electron acceptors and donors on transformation of tetrachloromethane by Shewanella putrefaciens MR-1. FEMS Microbiol Lett 121:357–364. https://doi.org/10.1111/j.1574-6968.1994.tb07126.x PubMed DOI
Rivera IG, Chowdhury MAR, Huq A, Jacobs D, Martins MT, Colwell RR (1995) Enterobacterial repetitive intergenic consensus sequences and PCR to generate fingerprints of genomic DNAs from Vibrio cholera O1, O139 and non-1 strains. Appl Environ Microbiol 61:2898–2904. https://doi.org/10.1128/aem.61.8.2898-2904.1995 PubMed DOI PMC
Salzberg SL, Delcher AL, Kasif S, White O (1998) Microbial gene identification using interpolated Markov models. Nucleic Acids Res 26:544–548. https://doi.org/10.1093/nar/26.2.544 PubMed DOI PMC
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. 3rd edn. Cold Spring Harbor, NY
Satomi M, Vogel BF, Venkateswaran K, Gram L (2007) Description of Shewanella glacialipiscicola sp. nov. and Shewanella algidipiscicola sp. nov., isolated from marine fish of the Danish Baltic Sea, and proposal that Shewanella affinis is a later heterotypic synonym of Shewanella colwelliana. Int J Syst Evol Microbiol 57:347–352. https://doi.org/10.1099/ijs.0.64708-0 PubMed DOI
Smibert RM, Krieg NR (1994) Phenotypic characterization. In Methods for general and molecular bacteriology, Edited by Gerhardt P, Murray RGE, Wood WA, Krieg NR. Washington, DC. Am Soc Microbiol. 607–655
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. https://doi.org/10.1093/bioinformatics/btu033 PubMed DOI PMC
Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin layer chromatography. Appl Environ Microbiol 28:226–231. https://doi.org/10.1128/am.28.2.226-231.1974 DOI
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569 PubMed DOI PMC
Venkateswaran K, Moser DP, Dollhopf ME, Lies DP, Saffarini DA, MacGregor BJ, Ringelberg DB, White DC, Nishijima M, Sano H, Burghardt J, Stackebrandt E, Nealson KH (1999) Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 49:705–724. https://doi.org/10.1099/00207713-49-2-705 PubMed DOI
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. https://doi.org/10.1371/journal.pone.0112963 PubMed DOI PMC
Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:e1005595. https://doi.org/10.1371/journal.pcbi.1005595 PubMed DOI PMC
Yang S-H, Kwon KK, Lee H-S, Kim S-J (2006) Shewanella spongiae sp. nov., isolated from a marine sponge. Int J Syst Evol Microbiol 56:2879–2882. https://doi.org/10.1099/ijs.0.64540-0 PubMed DOI