Brachybacterium kimchii sp. nov. and Brachybacterium halotolerans subsp. kimchii subsp. nov., isolated from the Korean fermented vegetables, kimchi, and description of Brachybacterium halotolerans subsp. halotolerans subsp. nov.

Brachybacterium halotolerans subsp. halotolerans Brachybacterium halotolerans subsp. kimchii Brachybacterium kimchii CBA3104T CBA3105T kimchi polyphasic taxonomy

Journal

Journal of microbiology (Seoul, Korea)
ISSN: 1976-3794
Titre abrégé: J Microbiol
Pays: Korea (South)
ID NLM: 9703165

Informations de publication

Date de publication:
Jul 2022
Historique:
received: 05 11 2021
accepted: 24 05 2022
revised: 19 05 2022
entrez: 5 7 2022
pubmed: 6 7 2022
medline: 7 7 2022
Statut: ppublish

Résumé

Two Gram-stain-positive, oxidase-negative, catalase-positive, and coccus-shaped bacterial strains, designated CBA3104

Identifiants

pubmed: 35781624
doi: 10.1007/s12275-022-1581-6
pii: 10.1007/s12275-022-1581-6
doi:

Substances chimiques

DNA, Bacterial 0
RNA, Ribosomal, 16S 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

678-688

Informations de copyright

© 2022. Author(s).

Références

Benson, H.J. 1994. Microbiological Applications: A Laboratory Manual in General Microbiology. 6th edn., Brown Publishers, London, United Kindom.
Cantalapiedra, C.P., Hernández-Plaza, A., Letunic, I., Bork, P., and Huerta-Cepas, J. 2021. eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829.
doi: 10.1093/molbev/msab293
Chen, M.S., Li, F.N., Chen, X.H., Yan, X.R., and Tuo, L. 2021. Brachybacterium halotolerans sp. nov., a halotolerant, endophytic actinomycete isolated from branch of Bruguiera gymnoirhiza. Antonie van Leeuwenhoek 114, 875–884.
doi: 10.1007/s10482-021-01565-z
Clark, K., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Sayers, E.W. 2016. GenBank. Nucleic Acids Res. 44, D67–D72.
doi: 10.1093/nar/gkv1276
Collins, M.D., Brown, J., and Jones, D. 1988. Brachybacterium faecium gen. nov., sp. nov., a coryneform bacterium from poultry deep litter. Int. J. Syst. Evol. Microbiol. 38, 45–48.
Felsenstein, J. 1981. Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution 35, 1229–1242.
doi: 10.1111/j.1558-5646.1981.tb04991.x
Fitch, W.M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20, 406–416.
doi: 10.2307/2412116
Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., and Tiedje, J.M. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91.
doi: 10.1099/ijs.0.64483-0
Groth, I., Schumann, P., Rajney, F.A., Martin, K., Schuetze, B., and Augsten, K. 1997. Bogoriella caseilytica gen. nov., sp. nov., a new alkaliphilic actinomycete from a soda lake in Africa. Int. J. Syst. Bacteriol. 47, 788–794.
doi: 10.1099/00207713-47-3-788
Hiraishi, A., Ueda, Y., Ishihara, J., and Mori, T. 1996. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J. Gen. Appl. Microbiol. 42, 457–469.
doi: 10.2323/jgam.42.457
Kanehisa, M. and Goto, S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30.
doi: 10.1093/nar/28.1.27
Kaur, G., Kumar, N., Mual, P., Kumar, A., Kumar, R.M., and Mayilraj, S. 2016. Brachybacterium aquaticum sp. nov., a novel actinobacterium isolated from seawater. Int. J. Syst. Evol. Microbiol. 66, 4705–4710.
doi: 10.1099/ijsem.0.001414
Lee, I., Chalita, M., Ha, S.M., Na, S.I., Yoon, S.H., and Chun, J. 2017. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int. J. Syst. Evol. Microbiol. 67, 2053–2057.
doi: 10.1099/ijsem.0.001872
Lee, I., Kim, Y.O., Park, S.C., and Chun, J. 2016. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 66, 1100–1103.
doi: 10.1099/ijsem.0.000760
Liu, Q.Q., Wang, Y., Li, J., Du, Z.J., and Chen, G.J. 2014a. Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans. Int. J. Syst. Evol. Microbiol. 64, 2204–2209.
doi: 10.1099/ijs.0.061986-0
Liu, Y., Xie, Q.Y., Shi, W., Li, L., An, J.Y., Zhao, Y.M., and Hong, K. 2014b. Brachybacterium huguangmaarense sp. nov., isolated from Lake sediment. Int. J. Syst. Evol. Microbiol. 64, 1673–1678.
doi: 10.1099/ijs.0.052464-0
Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.P., and Göker, M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14, 60.
doi: 10.1186/1471-2105-14-60
Miller, L.T. 1982. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J. Clin. Microbiol. 16, 584–586.
doi: 10.1128/jcm.16.3.584-586.1982
Ming, H., Cheng, L., Yi, B., Xia, T., Niu, M., Zhao, Z., Liu, B., Nie, G., and Cui, C. 2021. Brachybacterium subflavum sp. nov., a novel actinobacterium isolated from the foregut of grass carp. Int. J. Syst. Evol. Microbiol. 71. doi: https://doi.org/10.1099/ijsem.0.004839 .
Minnikin, D.E., O’donnell, A., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., and Parlett, J. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2, 233–241.
doi: 10.1016/0167-7012(84)90018-6
Page, A.J., Cummins, C.A., Hunt, M., Wong, V.K., Reuter, S., Holden, M.T.G., Fookes, M., Falush, D., Keane, J.A., and Parkhill, J. 2015. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691–3693.
doi: 10.1093/bioinformatics/btv421
Park, S.K., Kim, M.S., Jung, M.J., Nam, Y.D., Park, E.J., Roh, S.W., and Bae, J.W. 2011. Brachybacterium squillarum sp. nov., isolated from salt-fermented seafood. Int. J. Syst. Evol. Microbiol. 61, 1118–1122.
doi: 10.1099/ijs.0.022517-0
Parker, C.T., Tindall, B.J., and Garrity, G.M. 2019. International Code of Nomenclature of Prokaryotes. Int. J. Syst. Evol. Microbiol. 69, S1–S111.
doi: 10.1099/ijsem.0.000778
Parks, D.H., Imelfort, M., Skennerton, C.T., Hugenholtz, P., and Tyson, G.W. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055.
doi: 10.1101/gr.186072.114
Rice, P., Longden, I., and Bleasby, A. 2000. EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276–277.
doi: 10.1016/S0168-9525(00)02024-2
Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.
pubmed: 3447015
Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., Newark, Delaware, USA.
Schleifer, K.H. and Kandler, O. 1972. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol. Rev. 36, 407–477.
doi: 10.1128/br.36.4.407-477.1972
Schubert, K., Ludwig, W., Springer, N., Kroppenstedt, R.M., Accolas, J.P., and Fiedler, F. 1996. Two coryneform bacteria isolated from the surface of French Gruyère and Beaufort cheeses are new species of the genus Brachybacterium: Brachybacterium alimentarium sp. nov. and Brachybacterium tyrofermentans sp. nov. Int. J. Syst. Bacteriol. 46, 81–87.
doi: 10.1099/00207713-46-1-81
Seemann, T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069.
doi: 10.1093/bioinformatics/btu153
Singh, H., Du, J., Yang, J.E., Yin, C.S., Kook, M., and Yi, T.H. 2016. Brachybacterium horti sp. nov., isolated from garden soil. Int. J. Syst. Evol. Microbiol. 66, 189–195.
doi: 10.1099/ijsem.0.000696
Takeuchi, M., Fang, C.X., and Yokota, A. 1995. Taxonomic study of the genus Brachybacterium: Proposal of Brachybacterium conglomeratum sp. nov., nom. rev., Brachybacterium paraconglomeratum sp. nov., and Brachybacterium rhamnosum sp. nov. Int. J. Syst. Evol. Microbiol. 45, 160–168.
Tamura, K., Stecher, G., and Kumar, S. 2021. MEGA 11: molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38, 3022–3027.
doi: 10.1093/molbev/msab120
Thompson, J.D., Higgins, D.G., and Gibson, T.J. 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, 4673–4680.
doi: 10.1093/nar/22.22.4673
Tindall, B.J. 1990a. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst. Appl. Microbiol. 13, 128–130.
doi: 10.1016/S0723-2020(11)80158-X
Tindall, B.J. 1990b. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol. Lett. 66, 199–202.
doi: 10.1111/j.1574-6968.1990.tb03996.x
Tuo, L., Yan, X., Li, F., Bao, Y., Shi, H., Li, H., and Sun, C. 2018. Brachybacterium endophyticum sp. nov., a novel endophytic actinobacterium isolated from bark of Scutellaria baicalensis Georgi. Int. J. Syst. Evol. Microbiol. 68, 3563–3568.
doi: 10.1099/ijsem.0.003032
Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617.
doi: 10.1099/ijsem.0.001755

Auteurs

Yujin Kim (Y)

Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.

Yeon Bee Kim (YB)

Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.

Juseok Kim (J)

Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
Microbiome Research Team, LISCure Biosciences Inc., Seongnam, 13486, Republic of Korea.

Joon Yong Kim (JY)

Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
Microbiome Research Team, LISCure Biosciences Inc., Seongnam, 13486, Republic of Korea.

Tae Woong Whon (TW)

Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.

Won-Hyong Chung (WH)

Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea.

Eun-Ji Song (EJ)

Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea.

Young-Do Nam (YD)

Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea.

Se Hee Lee (SH)

Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea. leesehee@wikim.re.kr.

Seong Woon Roh (SW)

Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea. seong18@gmail.com.
Microbiome Research Team, LISCure Biosciences Inc., Seongnam, 13486, Republic of Korea. seong18@gmail.com.

Articles similaires

Genome, Chloroplast Phylogeny Genetic Markers Base Composition High-Throughput Nucleotide Sequencing

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Animals Hemiptera Insect Proteins Phylogeny Insecticides
Amaryllidaceae Alkaloids Lycoris NADPH-Ferrihemoprotein Reductase Gene Expression Regulation, Plant Plant Proteins

Classifications MeSH