Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, Klenk H-P, Schomburg D, Petersen J, Göker M (2017) Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J 11:1483–1499. https://doi.org/10.1038/ismej.2016.198
Article PubMed PubMed Central Google Scholar
Liang KYH, Orata FD, Boucher YF, Case RJ (2021) Roseobacters in a sea of poly- and paraphyly: whole genome-based taxonomy of the family Rhodobacteraceae and the proposal for the split of the Roseobacter clade into a novel family, Roseobacteraceae fam. nov. Front Microbiol 12:683109. https://doi.org/10.3389/fmicb.2021.683109
Article PubMed PubMed Central Google Scholar
Bakenhus I, Dlugosch L, Billerbeck S, Giebel H-A, Milke F, Simon M (2017) Composition of total and cell-proliferating bacterioplankton community in early summer in the North Sea – Roseobacters are the most active component. Front Microbiol 8:1771. https://doi.org/10.3389/fmicb.2017.1771
Article PubMed PubMed Central Google Scholar
Luo H, Moran MA (2014) Evolutionary ecology of the marine Roseobacter clade. Microbiol Mol Biol Rev 78:573–587. https://doi.org/10.1128/mmbr.00020-14
Article PubMed PubMed Central Google Scholar
Wagner-Döbler I, Biebl H (2006) Environmental biology of the marine Roseobacter lineage. Annu Rev Microbiol 60:255–280. https://doi.org/10.1146/annurev.micro.60.080805.142115
Article CAS PubMed Google Scholar
Jayan JN, Kim H-S, Srinivasan S, Kim H-S, Yu J-Y, Lee S-S (2024) Gilvirhabdus luticola gen. nov., sp. nov., a mesophilic and halophilic bacterium isolated from tidal flat sediment. Int J Syst Evol Microbiol 74:006474. https://doi.org/10.1099/ijsem.0.006474
Kang M-S, Yu J-Y, Kim H-S, Dong K, Srinivasan S, Lee S-S (2025) Meridianimarinicoccus marinus sp. nov., isolated from tidal flat. Curr Microbiol 82:197. https://doi.org/10.1007/s00284-025-04159-4
Article CAS PubMed Google Scholar
Jayan JN, Dong K, Srinivasan S, Lee S-S (2025) Sulfitobacter sediminis gen. nov., sp. nov., a novel halophilic bacterium isolated from tidal flat sediment. Int J Syst Evol Microbiol 75:006705. https://doi.org/10.1099/ijsem.0.006705
Jayan JN, Srinivasan S, Lee S-S (2025) Isolation and characterisation of Gracilimonas aurantiaca sp. nov., a novel bacterium isolated from tidal-flat sediment. Curr Microbiol 82:277. https://doi.org/10.1007/s00284-025-04257-3
Article CAS PubMed Google Scholar
Crenn K, Serpin D, Lepleux C, Overmann J, Jeanthon C (2016) Silicimonas algicola gen. nov., sp. nov., a member of the Roseobacter clade isolated from the cell surface of the marine diatom Thalassiosira delicatula. Int J Syst Evol Microbiol 66:4580–4588. https://doi.org/10.1099/ijsem.0.001394
Article CAS PubMed Google Scholar
Chalita M, Kim YO, Park S, Oh H-S, Cho JH, Moon J, Baek N, Moon C, Lee K, Yang J (2024) EzBioCloud: a genome-driven database and platform for microbiome identification and discovery. Int J Syst Evol Microbiol 74:006421. https://doi.org/10.1099/ijsem.0.006421-0
Article CAS PubMed PubMed Central Google Scholar
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Article CAS PubMed PubMed Central Google Scholar
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R (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
Thompson JD, Gibson TJ, Higgins DG (2003) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics:2.3.1–2.3.22. https://doi.org/10.1002/0471250953.bi0203s00
Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101:11030–11035. https://doi.org/10.1073/pnas.0404206101
Article CAS PubMed PubMed Central 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
Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics, Babraham Institute, Cambridge. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
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
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021
Article CAS PubMed PubMed Central Google Scholar
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M (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
Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H, Chun J (2017) ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 67:2053–2057. https://doi.org/10.1099/ijsem.0.001872
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
Kim D, Park S, Chun J (2021) Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 59:476–480. https://doi.org/10.1007/s12275-021-1125-7
Auch AF, von Jan M, Klenk H-P, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134. https://doi.org/10.4056/sigs.541628
Article PubMed PubMed Central Google Scholar
Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F, Alanjary M, Fetter A, Terlouw BR, Metcalf WW, Helfrich EJ (2023) antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acid Res 51:W46–W50. https://doi.org/10.1093/nar/gkad344
Article CAS PubMed PubMed Central 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 10:2182. https://doi.org/10.1038/s41467-019-10210-3
Article CAS PubMed PubMed Central Google Scholar
Middlebrook EA, Katani R, Fair JM (2024) OrthoPhyl—streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales. https://doi.org/10.1093/g3journal/jkae119. G3 14:jkae119
Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA, Krieg NR, Phillips GB (1981) Manual of methods for general bacteriology. American Society for Microbiology, Washington, DC
MacFaddin JF (2003) Pruebas bioquímicas para la identificación de bacterias de importancia clínica. Editorial Médica Panamericana, Madrid
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett J (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241. https://doi.org/10.1016/0167-7012(84)90018-6
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