Description of Roseibium sediminicola sp. nov. Isolated from Sediment of a Tidal Flat on the Yellow Sea Coast

Suzuki T, Muroga Y, Takahama M et al (2000) Roseigium denhamense gen. nov., sp. nov. and Roseibium hemelinense sp. nov., aerobic bacteriochlorophyll-containing bacteria isolated from the east and west coasts of Australia. Int J Syst Evol Microbiol 50:2151–2156. https://doi.org/10.1099/00207713-50-6-2151

Article  PubMed  Google Scholar 

Zhong ZP, Liu Y, Liu HC et al (2014) Roseibium aquae sp. nov., isolated from a saline lake. Int J Syst Evol Microbiol 64:2812–2818. https://doi.org/10.1099/ijs.0.065508-0

Article  CAS  PubMed  Google Scholar 

Liu J, Wang Y, Yang X et al (2017) Roseibium sediminis sp. nov., isolated from sea surface sediment. Int J Syst Evol Microbiol 67:2862–2867. https://doi.org/10.1099/ijsem.0.002034

Article  CAS  PubMed  Google Scholar 

Duan L, Li JL, Li X et al (2020) Roseibium aestuarii sp. nov., isolated from Pearl River Estuary. Int J Syst Evol Microbiol 70:2896–2900. https://doi.org/10.1099/ijsem.0.004116

Article  CAS  PubMed  Google Scholar 

Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. https://doi.org/10.1093/bioinformatics/btm404

Article  CAS  PubMed  Google Scholar 

Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054

Article  CAS  PubMed  PubMed Central  Google Scholar 

Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

Article  CAS  PubMed  Google Scholar 

Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 29:170–179. https://doi.org/10.1007/BF02100115

Article  CAS  PubMed  Google Scholar 

Czelusniak J, Goodman M, Moncrief ND et al (1990) Maximum parsimony approach to construction of evolutionary trees from aligned homologous sequences. Methods Enzymol 183:601–615. https://doi.org/10.1016/0076-6879(90)83039-c

Article  CAS  PubMed  Google Scholar 

Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/BF01731581

Article  CAS  PubMed  Google Scholar 

Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x

Article  PubMed  Google Scholar 

Brettin T, Davis JJ, Disz T et al (2015) RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365. https://doi.org/10.1038/srep08365

Article  CAS  PubMed  PubMed Central  Google Scholar 

Davis JJ, Wattam AR, Aziz RK et al (2020) The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res 48:606–612. https://doi.org/10.1093/nar/gkz943

Article  CAS  Google Scholar 

Huerta-Cepas J, Szklarczyk D, Heller D et al (2019) eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47:309–314. https://doi.org/10.1093/nar/gky1085

Article  CAS  Google Scholar 

Na SI, Kim YO, Yoon SH et al (2018) UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:281–285. https://doi.org/10.1007/s12275-018-8014-6

Article  CAS  Google Scholar 

Meier-Kolthoff JP, Auch AF, Klenk H-P et al (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinf 21:14–60. https://doi.org/10.1186/1471-2105-14-60

Article  Google Scholar 

Auch AF, Von Jan M, Klenk H-P et al (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genom Sci 2:117–134. https://doi.org/10.4056/sigs.531120

Article  Google Scholar 

Yoon SH, Ha SM, Lim J et al (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110(10):1281–1286. https://doi.org/10.1007/s10482-017-0844-4

Article  CAS  PubMed  Google Scholar 

Bernardet JF, Nakagawa Y, Holmes B (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

Article  CAS  PubMed  Google Scholar 

Cappuccino JG, Sherman N (2010) Microbiology: a laboratory manual, 9th edn. Benjamin Cummings, San Francisco

Google Scholar 

Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A (1981) Characteristics of the heterotrophic bacterial populations in hypersaline environments of different salt concentrations. Microb Ecol 7:235–243. https://doi.org/10.1007/BF02010306

Article  CAS  PubMed  Google Scholar 

Tindall BJ, Sikorski J, Smibert RA et al (2007) Phenotypic characterization and the principles of comparative systematics. Methods Gen Mol Microbiol. https://doi.org/10.1128/9781555817497.ch15

Article  Google Scholar 

da Costa MS, Albuquerque L, Nobre MF et al (2011) The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. Methods Microbiol 38:197–206. https://doi.org/10.1016/B978-0-12-387730-7.00009-7

Article  CAS  Google Scholar 

Piñeiro-Vidal M, Pazos F, Santos Y (2008) Fatty acid analysis as a chemotaxonomic tool for taxonomic and epidemiological characterization of four fish pathogenic Tenacibaculum species. Lett Appl Microbiol 46:548–554. https://doi.org/10.1111/j.1472-765X.2008.02348.x

Article  CAS  PubMed  Google Scholar 

Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44:846–849. https://doi.org/10.1099/00207713-44-4-846

Article  CAS  Google Scholar 

Stautz J, Hellmich Y, Fuss MF et al (2021) Molecular mechanisms for bacterial potassium homeostasis. J Mol Biol 433:166968. https://doi.org/10.1016/j.jmb.2021.166968

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yost CS (1999) Potassium channels: basic aspects, functional roles, and medical significance. Anesthesiology 90:1186–1203. https://doi.org/10.1097/00000542-199904000-00035

Article  CAS  PubMed  Google Scholar 

Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 106:19126–19131. https://doi.org/10.1073/pnas.0906412106

Article  PubMed  PubMed Central  Google Scholar 

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