Anaerocolumna sedimenticola sp. nov., isolated from fresh water sediment.

Bacterial Typing Techniques Base Composition Clostridiales DNA, Bacterial / genetics Fatty Acids / analysis Fresh Water Phospholipids / analysis Phylogeny RNA, Ribosomal, 16S / genetics Sequence Analysis, DNA
Anaerocolumna sedimenticola Bacteria New taxon The Geum River

Journal

Antonie van Leeuwenhoek
ISSN: 1572-9699
Titre abrégé: Antonie Van Leeuwenhoek
Pays: Netherlands
ID NLM: 0372625

Informations de publication

Date de publication:
May 2021
Historique:
received: 19 12 2020
accepted: 08 02 2021
pubmed: 18 3 2021
medline: 19 8 2021
entrez: 17 3 2021
Statut: ppublish

Résumé

Strain CBA3638

Identifiants

DOI: 10.1007/s10482-021-01536-4 PMID: 33730291
pubmed: 33730291
doi: 10.1007/s10482-021-01536-4
pii: 10.1007/s10482-021-01536-4
doi:

Substances chimiques

DNA, Bacterial 0
Fatty Acids 0
Phospholipids 0
RNA, Ribosomal, 16S 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

507-513

Subventions

Organisme : Nakdonggang National Institute of Biological Resources
ID : NNIBR201901213
Organisme : Ministry of Science and ICT
ID : KE2001-2
Organisme : National Research Foundation of Korea
ID : 2018R1D1A1A09082921

Références

Chin CS et al (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. https://doi.org/10.1038/nmeth.2474
doi: 10.1038/nmeth.2474 pubmed: 23644548
Chun J et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516
doi: 10.1099/ijsem.0.002516
Eitel Z, Soki J, Urban E, Nagy E, Infection ESGoA, (2013) The prevalence of antibiotic resistance genes in Bacteroides fragilis group strains isolated in different European countries. Anaerobe 21:43–49. https://doi.org/10.1016/j.anaerobe.2013.03.001
doi: 10.1016/j.anaerobe.2013.03.001 pubmed: 23500457
Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 39:224–229. https://doi.org/10.1099/00207713-39-3-224
doi: 10.1099/00207713-39-3-224
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
doi: 10.1007/BF01734359 pubmed: 7288891
Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416. https://doi.org/10.1093/sysbio/20.4.406
doi: 10.1093/sysbio/20.4.406
Jaime H et al (2019) eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47:D309–D314. https://doi.org/10.1093/nar/gky1085
doi: 10.1093/nar/gky1085
Jeong H, Yi H, Sekiguchi Y, Muramatsu M, Kamagata Y, Chun J (2004) Clostridium jejuense sp. nov., isolated from soil. Int J Syst Evol Microbiol 54:1465–1468. https://doi.org/10.1099/ijs.0.63128-0
doi: 10.1099/ijs.0.63128-0 pubmed: 15388696
Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428:726–731. https://doi.org/10.1016/j.jmb.2015.11.006
doi: 10.1016/j.jmb.2015.11.006 pubmed: 26585406
Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
doi: 10.1093/molbev/msw054
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12. https://doi.org/10.1186/gb-2004-5-2-r12
doi: 10.1186/gb-2004-5-2-r12 pubmed: 395750 pmcid: 395750
Lane D (1991) 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics pp 115–175
Lee I, Ouk Kim Y, 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
doi: 10.1099/ijsem.0.000760 pubmed: 26585518
Lee I, Chalita M, Ha SM, Na SI, Yoon SH, 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
doi: 10.1099/ijsem.0.001872 pubmed: 28639931
Lee C, Kim JY, Kim YB, Kim J, Ahn SW, Song HS, Roh SW (2020) A report of 37 unrecorded anaerobic bacterial species isolated from the Geum River in South Korea. J Species Res 9:105–116. https://doi.org/10.12651/JSR.2020.9.2.105
doi: 10.12651/JSR.2020.9.2.105
Mechichi T, Labat M, Garcia JL, Thomas P, Patel BK (1999) Characterization of a new xylanolytic bacterium, Clostridium xylanovorans sp. nov. Syst Appl Microbiol 22:366–371. https://doi.org/10.1016/S0723-2020(99)80044-7
doi: 10.1016/S0723-2020(99)80044-7 pubmed: 10553289
Minnikin D, O’donnell A, 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
doi: 10.1016/0167-7012(84)90018-6
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
doi: 10.1093/oxfordjournals.molbev.a040454 pubmed: 3447015 pmcid: 3447015
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI technical note 101. Newark, DE: MIDI inc
Tatusova T et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569
doi: 10.1093/nar/gkw569 pubmed: 27342282 pmcid: 5001611
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 22:4673–4680. https://doi.org/10.1093/nar/22.22.4673
doi: 10.1093/nar/22.22.4673 pubmed: 308517 pmcid: 308517
Ueki A, Ohtaki Y, Kaku N, Ueki K (2016) Descriptions of Anaerotaenia torta gen. nov., sp. nov. and Anaerocolumna cellulosilytica gen. nov., sp. nov. isolated from a methanogenic reactor of cattle waste and reclassification of Clostridium aminovalericum, Clostridium jejuense and Clostridium xylanovorans as Anaerocolumna species. Int J Syst Evol Microbiol 66:2936–2943. https://doi.org/10.1099/ijsem.0.001123
doi: 10.1099/ijsem.0.001123 pubmed: 27126251
Varela-Álvarez E et al (2006) Genomic DNA isolation from green and brown algae (caulerpales and fucales) for microsatellite library construction. J Phycol 42:741–745. https://doi.org/10.1111/j.1529-8817.2006.00218.x
doi: 10.1111/j.1529-8817.2006.00218.x
Wayne LG (1988) International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Zentralbl Bakteriol Mikrobiol Hyg A 268:433–434. https://doi.org/10.1016/s0176-6724(88)80120-2
doi: 10.1016/s0176-6724(88)80120-2 pubmed: 3213314
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, 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. https://doi.org/10.1099/ijsem.0.001755
doi: 10.1099/ijsem.0.001755 pubmed: 28005526 pmcid: 28005526

Auteurs

Juseok Kim (J)

Microbiology and Functionality Research Group and Industrial Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
Division of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.

Joon Yong Kim (JY)

Microbiology and Functionality Research Group and Industrial Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.

Hye Seon Song (HS)

Microbiology and Functionality Research Group and Industrial Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.

Yeon Bee Kim (YB)

Microbiology and Functionality Research Group and Industrial Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.

Tae Woong Whon (TW)

Microbiology and Functionality Research Group and Industrial Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.

Seung Woo Ahn (SW)

Microbiology and Functionality Research Group and Industrial Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
Division of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.

Se Hee Lee (SH)

Microbiology and Functionality Research Group and Industrial Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.

SeungRan Yoo (S)

Microbiology and Functionality Research Group and Industrial Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.

Yu Jin Kim (YJ)

Microbiology and Functionality Research Group and Industrial Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.

Jinjong Myoung (J)

Korea Zoonosis Research Institute, Chonbuk National University, Jeollabuk-do, 54531, Republic of Korea.

Yoon-E Choi (YE)

Division of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.

Hong-Seok Son (HS)

Department of Food Biosciences and Technology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea. sonhs@korea.ac.kr.

Seong Woon Roh (SW)

Microbiology and Functionality Research Group and Industrial Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea. seong18@gmail.com.
ORCID: 0000-0003-0609-6130

Articles similaires

Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences.

Yue Zhang, Meifang Song, Deying Tang et al.
1.00
Genome, Chloroplast Phylogeny Genetic Markers Base Composition High-Throughput Nucleotide Sequencing

Decoding the genomic terrain: functional insights into 14 chemosensory proteins in whitefly Bemisia tabaci Asia II-1.

M N Rudra Gouda, Sabtharishi Subramanian
1.00
Animals Hemiptera Insect Proteins Phylogeny Insecticides

Multiple NADPH-cytochrome P450 reductases from Lycoris radiata involved in Amaryllidaceae alkaloids biosynthesis.

Yuqing Wu, Yifeng Zhang, Haitong Fan et al.
1.00
Amaryllidaceae Alkaloids Lycoris NADPH-Ferrihemoprotein Reductase Gene Expression Regulation, Plant Plant Proteins

Fasciola hepatica and Fasciola hybrid form co-existence in yak from Tibet of China: application of rDNA internal transcribed spacer.

Wenqiang Tang, Yule Zhou, Leyi Li et al.
1.00
Animals Cattle Tibet Fasciola Fascioliasis

Classifications MeSH

questionsmedicales.fr › Techniques d'investigation › Techniques de laboratoire clinique › Techniques microbiologiques › Techniques bactériologiques › Techniques de typage bactérien › Anaerocolumna sedimenticola sp. nov., isolated...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Composition en bases nucléiques › Anaerocolumna sedimenticola sp. nov., isolated...
questionsmedicales.fr › Bactéries › Firmicutes › Clostridiales › Anaerocolumna sedimenticola sp. nov., isolated...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › ADN bactérien › Anaerocolumna sedimenticola sp. nov., isolated...
questionsmedicales.fr › Lipides › Acides gras › Anaerocolumna sedimenticola sp. nov., isolated...
questionsmedicales.fr › Environnement et santé publique › Environnement › Eau douce › Anaerocolumna sedimenticola sp. nov., isolated...
questionsmedicales.fr › Lipides › Lipides membranaires › Phospholipides › Anaerocolumna sedimenticola sp. nov., isolated...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Anaerocolumna sedimenticola sp. nov., isolated...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN ribosomique › ARN ribosomique 16S › Anaerocolumna sedimenticola sp. nov., isolated...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Anaerocolumna sedimenticola sp. nov., isolated...