Phylogeny and genomic analysis of Shewanella cutis sp. nov., isolated from freshwater pufferfish

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  PubMed  Google Scholar 

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

Article  CAS 

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