Strain identifier
BacDive ID: 23808
Type strain: 
Species: Brevibacterium daeguense
Strain Designation: 2C6-41, 2C6-41N
Strain history: <- MJ Lee, H-Plus Eco, Korea
NCBI tax ID(s): 909936 (species)
version 8.1 (current version)
General
@ref: 20482
BacDive-ID: 23808
DSM-Number: 27938
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive
description: Brevibacterium daeguense 2C6-41 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from activated sludge from industrial wastewater treatment plant.
NCBI tax id
- NCBI tax id: 909936
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20482 | <- JCM; JCM 17458 <- S. T. Lee, KAIST; 2C6-41 |
| 67770 | S.-T. Lee 2C6-41. |
| 67771 | <- MJ Lee, H-Plus Eco, Korea |
doi: 10.13145/bacdive23808.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Brevibacteriaceae
- genus: Brevibacterium
- species: Brevibacterium daeguense
- full scientific name: Brevibacterium daeguense Cui et al. 2013
@ref: 20482
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Brevibacteriaceae
genus: Brevibacterium
species: Brevibacterium daeguense
full scientific name: Brevibacterium daeguense Cui et al. 2013
strain designation: 2C6-41, 2C6-41N
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | motility |
|---|---|---|---|---|
| 30529 | positive | 1.125 µm | 0.65 µm | no |
| 67771 | positive |
Culture and growth conditions
culture medium
- @ref: 20482
- name: RICH MEDIUM (DSMZ Medium 736)
- growth: yes
- link: https://mediadive.dsmz.de/medium/736
- composition: Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20482 | positive | growth | 28 | mesophilic |
| 30529 | positive | growth | 10-42 | |
| 30529 | positive | optimum | 26 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 30529 | aerobe |
| 67771 | aerobe |
spore formation
- @ref: 30529
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30529 | NaCl | positive | growth | 0-5 % |
| 30529 | NaCl | positive | optimum | 2.5 % |
observation
| @ref | observation |
|---|---|
| 67770 | quinones: MK-8(H2) |
| 67771 | quinones: MK-8(H2) |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30529 | 37054 | 3-hydroxybutyrate | + | carbon source |
| 30529 | 30089 | acetate | + | carbon source |
| 30529 | 17128 | adipate | + | carbon source |
| 30529 | 24265 | gluconate | + | carbon source |
| 30529 | 28087 | glycogen | + | carbon source |
| 30529 | 24996 | lactate | + | carbon source |
| 30529 | 25115 | malate | + | carbon source |
| 30529 | 9300 | suberic acid | + | carbon source |
| 30529 | 31011 | valerate | + | carbon source |
| 30529 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 30529
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 20482 | activated sludge from industrial wastewater treatment plant | Daegu | Republic of Korea | KOR | Asia |
| 67770 | Activated sludge from an industrial wastewater treatment plant | Daegu | Republic of Korea | KOR | Asia |
| 67771 | From the activated sludge, an industrial wastewater treatment plant | Daegu | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Waste | #Activated sludge |
| #Engineered | #Waste | #Industrial wastewater |
| #Engineered | #Waste | #Water treatment plant |
taxonmaps
- @ref: 69479
- File name: preview.99_150294.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15817;96_1988;97_73812;98_99326;99_150294&stattab=map
- Last taxonomy: Brevibacterium daeguense subclade
- 16S sequence: HQ246162
- Sequence Identity:
- Total samples: 714
- soil counts: 189
- aquatic counts: 64
- animal counts: 435
- plant counts: 26
Safety information
risk assessment
- @ref: 20482
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20482
- description: Brevibacterium daeguense strain 2C6-41 16S ribosomal RNA gene, partial sequence
- accession: HQ246162
- length: 1365
- database: ena
- NCBI tax ID: 909936
Genome sequences
- @ref: 66792
- description: Brevibacterium daeguense DSM 27938
- accession: GCA_021729135
- assembly level: contig
- database: ncbi
- NCBI tax ID: 909936
GC content
| @ref | GC-content | method |
|---|---|---|
| 20482 | 66.4 | high performance liquid chromatography (HPLC) |
| 30529 | 66.4 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | no | 98.814 | no |
| gram-positive | yes | 93.175 | no |
| anaerobic | no | 99.137 | no |
| aerobic | yes | 95.67 | yes |
| halophile | no | 55.231 | no |
| spore-forming | no | 93.581 | no |
| motile | no | 90.688 | no |
| glucose-ferment | no | 94.35 | no |
| thermophile | no | 98.607 | yes |
| glucose-util | yes | 80.24 | no |
External links
@ref: 20482
culture collection no.: DSM 27938, JCM 17458, KCTC 19800
straininfo link
- @ref: 87838
- straininfo: 401727
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22368170 | Brevibacterium daeguense sp. nov., a nitrate-reducing bacterium isolated from a 4-chlorophenol enrichment culture. | Cui Y, Kang MS, Woo SG, Jin L, Kim KK, Park J, Lee M, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.038141-0 | 2012 | Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Brevibacterium/*classification/genetics/isolation & purification/metabolism, Carbohydrates/analysis, *Chlorophenols, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nitrates/*metabolism, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Metabolism |
| Phylogeny | 23543497 | Brevibacterium jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. | Choi EJ, Lee SH, Jung JY, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.049197-0 | 2013 | Base Composition, Brevibacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, *Fermentation, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seafood/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Phylogeny | 32816658 | Brevibacterium rongguiense sp. nov., isolated from freshwater sediment. | Deng T, Lu H, Qian Y, Chen X, Yang X, Guo J, Sun G, Xu M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004379 | 2020 | Bacterial Typing Techniques, Base Composition, Brevibacterium/*classification/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 20482 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27938 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27938) | |||
| 30529 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26861 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 87838 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID401727.1 |