Skerman VBD, McGowan V, Sneath PHA (1980) Approved lists of bacterial names. Int J Syst Bacteriol 30(1):225–420. https://doi.org/10.1099/00207713-30-1-225

Article  Google Scholar 

Parte AC, Sardà Carbasse 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 70:5607–5612. https://doi.org/10.1099/ijsem.0.004332

Article  PubMed  PubMed Central  Google Scholar 

Vallet-Gely I, Novikov A, Augusto L, Liehl P, Bolbach G, Péchy-Tarr M (2010) Association of hemolytic activity of Pseudomonas entomophila, a versatile soil bacterium, with cyclic lipopeptide production. Appl Environ Microbiol 76(3):910–921. https://doi.org/10.1128/AEM.02112-09

Article  CAS  PubMed  Google Scholar 

Höfte M, De Vos P (2007) Plant pathogenic Pseudomonas species. In: Gnanamanickam SS (ed) Plant-associated bacteria. Springer, Dordrecht, pp 507–533. https://doi.org/10.1007/978-1-4020-4538-7_14.

Chapter  Google Scholar 

Girard L, Lood C, Höfte M, Vandamme P, Rokni-Zadeh H, van Noort V (2021) The ever-expanding Pseudomonas genus: description of 43 new species and partition of the Pseudomonas putida group. Microorganisms 9(8):1766. https://doi.org/10.3390/microorganisms9081766

Article  CAS  PubMed  PubMed Central  Google Scholar 

Viggor S, Jõesaar M, Vedler E, Kiiker R, Pärnpuu L, Heinaru A (2015) Occurrence of diverse alkane hydroxylase AlkB genes in indigenous oil-degrading bacteria of Baltic Sea surface water. Mar Pollut Bull 101(2):507–516. https://doi.org/10.1016/j.marpolbul.2015.10.064

Article  CAS  PubMed  Google Scholar 

Rudra B, Duncan L, Shah AJ, Shah HN, Gupta RS (2022) Phylogenomic and comparative genomic studies robustly demarcate two distinct clades of Pseudomonas aeruginosa strains: proposal to transfer the strains from an outlier clade to a novel species Pseudomonas paraeruginosa sp. nov. Int J Syst Evol Microbiol 72(11):005542. https://doi.org/10.1099/ijsem.0.005542

Article  CAS  Google Scholar 

Beaton A, Lood C, Cunningham-Oakes E, MacFadyen A, Mullins AJ, Bestawy WE (2018) Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica A390T sequenced by ion semiconductor and nanopore technologies. FEMS Microbiol Lett 365(12):fny069. https://doi.org/10.1093/femsle/fny069

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wasi S, Tabrez S, Ahmad M (2013) Use of Pseudomonas spp. for the bioremediation of environmental pollutants: a review. Environ Monit Assess 185(10):8147–8155. https://doi.org/10.1007/s10661-013-3163-x

Article  PubMed  Google Scholar 

Weller DM (2007) Pseudomonas biocontrol agents of soilborne pathogens: looking back over 30 years. Phytopathology 97(2):250–256. https://doi.org/10.1094/PHYTO-97-2-0250

Article  PubMed  Google Scholar 

Frasson D, Opoku M, Picozzi T, Torossi T, Balada S, Smits THM, Hilber U (2017) Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidholzensis sp. nov., two novel species within the Pseudomonas putida group isolated from forest soil. Int J Syst Evol Microbiol 67(8):2853–2861. https://doi.org/10.1099/ijsem.0.002035

Article  CAS  PubMed  Google Scholar 

Rudra B, Gupta RS (2023) Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera. Front Microbiol 14:1273665. https://doi.org/10.3389/fmicb.2023.1273665

Article  PubMed  Google Scholar 

Oren A, Göker M (2024) Validation List 219. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 74:6452

Google Scholar 

He H, Wang Y, Li BY, Lu CY, Li S, Zheng ZH et al (2025) Altererythrobacter guangdongensis sp. nov. and Tsuneonella sediminis sp. nov., two novel carotenoid-producing species isolated from tidal flat sediment. Syst Appl Microbiol 48:126649

Article  CAS  PubMed  Google Scholar 

Brosius J, Palmer ML, Kennedy PJ, Noller HF (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 75(10):4801–4805. https://doi.org/10.1073/pnas.75.10.4801

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67(5):1613–1617

Article  CAS  PubMed  PubMed Central  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  CAS  PubMed  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  CAS  PubMed  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  CAS  PubMed  Google Scholar 

Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18(1):1–32. https://doi.org/10.2307/2412407

Article  Google Scholar 

Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C (2017) Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 45(D1):D535–D542. https://doi.org/10.1093/nar/gkw1017

Article  CAS  PubMed  Google Scholar 

Chklovski A, Parks DH, Woodcroft BJ et al (2023) CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods Nat Methods 20:1203–1212. https://doi.org/10.1038/s41592-023-01940-w

Article  CAS  PubMed  Google Scholar 

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA (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 

Kim J, Na SI, Kim D, Chun J (2021) UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 59(6):609–615

Article  CAS  PubMed  Google Scholar 

Meier-Kolthoff JP, Goker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10(1):2182

Article  PubMed  PubMed Central  Google Scholar 

Lee I, Kim YO, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760

Article  CAS  PubMed  Google Scholar 

Rodriguez-R LM, Konstantinidis KT (2016) The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ 4:e1900v1 https://doi.org/10.7287/peerj.preprints.1900v1

Article  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 Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60

Article  PubMed  PubMed Central  Google Scholar 

Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45(D1):D353–D361. https://doi.org/10.1093/nar/gkw1092

Article  CAS  PubMed  Google Scholar 

Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP, Medema MH (2021) antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 49(W1):W29–35. https://doi.org/10.1093/nar/gkab335