Denner EB, Smith GW, Busse HJ et al (2003) Aurantimonas coralicida gen nov, sp nov, the causative agent of white plague type II on Caribbean scleractinian corals. Int J Syst Evol Microbiol 53:1115–1122. https://doi.org/10.1099/ijs.0.02359-0
Article CAS PubMed Google Scholar
Du J, Zhang Y, Xin D et al (2023) Antarcticirhabdus aurantiaca gen nov, sp nov, isolated from Antarctic gravel soil. Int J Syst Evol Microbiol 73:005814. https://doi.org/10.1099/ijsem.0.005814
Rathsack K, Reitner J, Stackebrandt E et al (2011) Reclassification of Aurantimonas altamirensis (Jurado et al 2006), Aurantimonas ureilytica (Weon et al 2007) and Aurantimonas frigidaquae (Kim et al 2008) as members of a new genus, Aureimonas gen nov, as Aureimonas altamirensis gen nov, comb nov, Aureimonas ureilytica comb nov and Aureimonas frigidaquae comb nov, and emended descriptions of the genera Aurantimonas and Fulvimarina. Int J Syst Evol Microbiol 61:2722–2728. https://doi.org/10.1099/ijs.0.027029-0
Article CAS PubMed Google Scholar
Díaz-Cárdenas C, Bernal LF, Caro-Quintero A et al (2017) Draft genome and description of Consotaella salsifontis gen. nov. sp. nov a halophilic, free-living, nitrogen-fixing alphaproteobacterium isolated from an ancient terrestrial saline spring. Int J Syst Evol Microbiol 67(10):3744–3751. https://doi.org/10.1099/ijsem.0.002185
Article CAS PubMed Google Scholar
Cho JC, Giovannoni SJ (2003) Fulvimarina pelagi gen nov, sp nov, a marine bacterium that forms a deep evolutionary lineage of descent in the order “Rhizobiales”. Int J Syst Evol Microbiol 53:1853–1859. https://doi.org/10.1099/ijs.0.02644-0
Article CAS PubMed Google Scholar
Jiang L, Peng Y, Kim KH et al (2023) Jeongeuplla avenae gen. nov., sp. nov., a novel β-carotene-producing bacterium that alleviates salinity stress in Arabidopsis. Front Microbiol 14:1265308. https://doi.org/10.3389/fmicb.2023.1265308
Article PubMed PubMed Central Google Scholar
Liang J, Liu J, Zhang XH (2015) Jiella aquimaris gen nov, sp nov, isolated from offshore surface seawater. Int J Syst Evol Microbiol 65:1127–1132. https://doi.org/10.1099/ijs.0.000067
Article CAS PubMed Google Scholar
Li FN, Liao S, Guo M et al (2018) Mangrovicella endophytica gen nov, sp nov, a new member of the family Aurantimonadaceae isolated from Aegiceras corniculatum. Int J Syst Evol Microbiol 68:2838–2845. https://doi.org/10.1099/ijsem.0.002907
Article CAS PubMed Google Scholar
Liu J, Gao CH, Han Y et al (2017) Nocardioides kandeliae sp. nov., an endophytic actinomycete isolated from leaves of Kandelia candel. Int J Syst Evol Microbiol 67:3888–3893. https://doi.org/10.1099/ijsem.0.002218
Article CAS PubMed Google Scholar
Bai X, Xiong Y, Lu S et al (2016) Streptococcus pantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii). Int J Syst Evol Microbiol 66:3281–3286. https://doi.org/10.1099/ijsem.0.001189
Article CAS PubMed Google Scholar
Yoon SH, Ha SM, Kwon S et al (2017) Introducing ezbiocloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755
Article CAS PubMed PubMed Central 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) MEGA 7: 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
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Article CAS PubMed Google Scholar
Fitch W (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416. https://doi.org/10.1093/sysbio/20.4.406
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequence. 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
Lim HJ, Lee EH, Yoon Y et al (2016) Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 120:379–387. https://doi.org/10.1111/jam.13011
Article CAS PubMed Google Scholar
Li R, Li Y, Kristiansen K et al (2008) Soap: short oligonucleotide alignment program. Bioinformatics 24:713–714. https://doi.org/10.1093/bioinformatics/btn025
Article CAS PubMed Google Scholar
Luo R, Liu B, Xie Y et al (2012) Soapdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18. https://doi.org/10.1186/2047-217X-1-18
Article 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:D606–D612. https://doi.org/10.1093/nar/gkz943
Article CAS PubMed Google Scholar
Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75
Article CAS PubMed PubMed Central Google Scholar
Tian R, Imanian B (2023) VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution. Microbiome 11:247. https://doi.org/10.1186/s40168-023-01705-9
Article CAS PubMed PubMed Central Google Scholar
Meier-Kolthoff JP, Sardà Carbasse J, Peinado-Olarte RL et al (2022) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acid Res 50:D801–D807. https://doi.org/10.1093/nar/gkab902
Article CAS PubMed Google Scholar
Yoon SH, Ha SM, Lim JM et al (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4
Article CAS PubMed Google Scholar
Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe 9:111–118
Kelly KL (1964) Inter-society color council-national bureau of standards color name charts illustrated with centroid colors. US Government Printing Office, Washington
Xu P, Li WJ, Tang SK et al (2005) Naxibacter alkalitolerans gen nov, sp nov, a novel member of the family ‘oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153. https://doi.org/10.1099/ijs.0.63407-0
Comments (0)