Strain identifier
BacDive ID: 140077
Type strain: 
Species: Brachybacterium ginsengisoli
Strain history: <- Deok-Chun Yang, Kyung Hee Univ.
NCBI tax ID(s): 1331682 (species)
version 9.3 (current version)
General
@ref: 42684
BacDive-ID: 140077
DSM-Number: 105781
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic
description: Brachybacterium ginsengisoli DSM 105781 is an aerobe, mesophilic bacterium that was isolated from Soil of a ginseng field.
NCBI tax id
- NCBI tax id: 1331682
- Matching level: species
strain history
| @ref | history |
|---|---|
| 42684 | <- JCM, RIKEN Bioresource Center, Tsukuba, Japan; JCM 19356 <- Y.-J. Kim, Kyung Hee University, Gyeonggi-do, South Korea; DCY80 |
| 67770 | Y.-J. Kim and D.-C. Yang DCY80. |
| 67771 | <- Deok-Chun Yang, Kyung Hee Univ. |
doi: 10.13145/bacdive140077.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Dermabacteraceae
- genus: Brachybacterium
- species: Brachybacterium ginsengisoli
- full scientific name: Brachybacterium ginsengisoli Hoang et al. 2014
@ref: 42684
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Dermabacteraceae
genus: Brachybacterium
species: Brachybacterium ginsengisoli
full scientific name: Brachybacterium ginsengisoli Hoang et al. 2014
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 125438 | no | 91.5 | |
| 125438 | 92.712 | positive |
Culture and growth conditions
culture medium
- @ref: 42684
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 42684 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
| 67771 | positive | growth | 25 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
observation
- @ref: 67770
- observation: quinones: MK-7, MK-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 42684 | Soil of a ginseng field | Yeoncheon Province | Republic of Korea | KOR | Asia |
| 67770 | Soil of a ginseng field in Yeoncheon Province | Republic of Korea | KOR | Asia | |
| 67771 | From ginseng soil | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_71187.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1217;97_1443;98_1761;99_71187&stattab=map
- Last taxonomy: Brachybacterium
- 16S sequence: KC876052
- Sequence Identity:
- Total samples: 834
- soil counts: 96
- aquatic counts: 58
- animal counts: 648
- plant counts: 32
Safety information
risk assessment
- @ref: 42684
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 42684
- description: Brachybacterium ginsengisoli strain DCY80 16S ribosomal RNA gene, partial sequence
- accession: KC876052
- length: 1416
- database: nuccore
- NCBI tax ID: 1331682
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Brachybacterium ginsengisoli strain DCY80 | 1331682.4 | complete | patric | 1331682 |
| 67770 | Brachybacterium ginsengisoli DCY80 | GCA_002407065 | complete | ncbi | 1331682 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 42684 | 71.0 | high performance liquid chromatography (HPLC) |
| 67770 | 71 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 92.712 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.29 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 67.415 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 83.562 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 93.417 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 91.5 | no |
External links
@ref: 42684
culture collection no.: DSM 105781, JCM 19356, KCTC 29226, DCY 80
straininfo link
- @ref: 96490
- straininfo: 398243
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24944333 | Brachybacterium ginsengisoli sp. nov., isolated from soil of a ginseng field. | Hoang VA, Kim YJ, Nguyen NL, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.058388-0 | 2014 | Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 30131788 | Phenotypic and Genomic Properties of Brachybacterium vulturis sp. nov. and Brachybacterium avium sp. nov. | Tak EJ, Kim PS, Hyun DW, Kim HS, Lee JY, Kang W, Sung H, Shin NR, Kim MS, Whon TW, Bae JW | Front Microbiol | 10.3389/fmicb.2018.01809 | 2018 |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 42684 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-105781 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105781) | |
| 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/ | |
| 96490 | 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-ID398243.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |