Reclassification of Salisediminibacterium haloalkalitolerans Sultanpuram et al. 2015 as a Later Heterotypic Synonym of Salisediminibacterium halotolerans Jiang et al. 2012

Jiang F, Cao SJ, Li Z-H, Fan H, Li HF, Liu WJ, Yuan HL (2012) Salisediminibacterium halotolerans gen. nov., sp. nov., a halophilic bacterium from soda lake sediment. Int J Syst Evol Microbiol 62(Pt_9):2127–2132. https://doi.org/10.1099/ijs.0.034488-0

Article  PubMed  Google Scholar 

Sultanpuram VR, Mothe T, Mohammed F (2015) Salisediminibacterium haloalkalitolerans sp. nov., isolated from Lonar soda lake, India, and a proposal for reclassification of Bacillus locisalis as Salisediminibacterium locisalis comb. nov., and the emended description of the genus Salisediminibacterium and of the species Salisediminibacterium halotolerans. Arch Microbiol 197(4):553–560. https://doi.org/10.1007/s00203-015-1081-8

Gupta RS, Patel S, Saini N, Chen S (2020) Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 70(11):5753–5798. https://doi.org/10.1099/ijsem.0.004475

Parte AC, SardàCarbasse J, Meier-Kolthoff JP, Reimer LC, Göker M (2020) List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70(11):5607–5612. https://doi.org/10.1099/ijsem.0.004332

Article  PubMed  PubMed Central  Google Scholar 

Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37(4):463–464. https://doi.org/10.1099/00207713-37-4-463

Article  Google Scholar 

Auch AF, von Jan M, Klenk HP, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2(1):117–134. https://doi.org/10.4056/sigs.531120

Article  PubMed  PubMed Central  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(7):1043–1055. https://doi.org/10.1101/gr.186072.114

Article  PubMed  PubMed Central  CAS  Google Scholar 

Seemann T (2013) barrnap 0.9: rapid ribosomal RNA prediction. https://github.com/tseemann/barrnap

Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680. https://doi.org/10.1093/nar/22.22.4673

Article  PubMed  PubMed Central  CAS  Google Scholar 

Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874. https://doi.org/10.1093/molbev/msw054

Article  PubMed  PubMed Central  CAS  Google Scholar 

Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376. https://doi.org/10.1007/bf01734359

Article  PubMed  CAS  Google Scholar 

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

Article  PubMed  CAS  Google Scholar 

Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20(4):406–416. https://doi.org/10.1093/sysbio/20.4.406

Article  Google Scholar 

Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x

Article  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(2):111–120. https://doi.org/10.1007/BF01731581

Article  PubMed  CAS  Google Scholar 

Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York

Book  Google Scholar 

Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO (2015) Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3:e1319. https://doi.org/10.7717/peerj.1319

Article  PubMed  PubMed Central  Google Scholar 

Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, Fink I, Pan JN, Yousef M, Fogarty EC, Trigodet F, Watson AR, Esen ÖC, Moore RM, Clayssen Q, Lee MD, Kivenson V, Graham ED, Merrill BD, Karkman A, Blankenberg D, Eppley JM, Sjödin A, Scott JJ, Vázquez-Campos X, McKay LJ, McDaniel EA, Stevens SLR, Anderson RE, Fuessel J, Fernandez-Guerra A, Maignien L, Delmont TO, Willis AD (2021) Community-led, integrated, reproducible multi-omics with anvi’o. Nat Microbiol 6(1):3–6. https://doi.org/10.1038/s41564-020-00834-3

Article  PubMed  PubMed Central  CAS  Google Scholar 

Price MN, Dehal PS, Arkin AP (2010) FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One 5(3):e9490. https://doi.org/10.1371/journal.pone.0009490

Article  PubMed  PubMed Central  CAS  Google Scholar 

Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf 11(1):119. https://doi.org/10.1186/1471-2105-11-119

Article  CAS  Google Scholar 

Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7(10):e1002195. https://doi.org/10.1371/journal.pcbi.1002195

Article  PubMed  PubMed Central  CAS  Google Scholar 

Lee MD (2019) GToTree: a user-friendly workflow for phylogenomics. Bioinformatics 35(20):4162–4164. https://doi.org/10.1093/bioinformatics/btz188

Article  PubMed  PubMed Central  CAS  Google Scholar 

Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797. https://doi.org/10.1093/nar/gkh340

Article  PubMed  PubMed Central  CAS  Google Scholar 

Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10(1):2182. https://doi.org/10.1038/s41467-019-10210-3

Article  PubMed  PubMed Central  CAS  Google Scholar 

Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108. https://doi.org/10.1093/nar/gkm160

Article  PubMed  PubMed Central  CAS  Google Scholar 

Lefort V, Desper R, Gascuel O (2015) FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 32(10):2798–2800. https://doi.org/10.1093/molbev/msv150

Article  PubMed  PubMed Central  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 Bioinf 14:60. https://doi.org/10.1186/1471-2105-14-60

Article  Google Scholar 

Kreft L, Botzki A, Coppens F, Vandepoele K, Van Bel M (2017) PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. Bioinformatics 33(18):2946–2947. https://doi.org/10.1093/bioinformatics/btx324

Article  PubMed  CAS  Google Scholar 

Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK (2016) Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 8(1):12–24. https://doi.org/10.1039/C5AY02550H

Article  Google Scholar 

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421. https://doi.org/10.1186/1471-2105-10-421

Article  PubMed  PubMed Central  CAS 

Comments (0)

No login
gif