Strain identifier
BacDive ID: 7455
Type strain:
Species: Microbacterium ginsengiterrae
Strain history: <- DC Yang, Kyunghee Univ.
NCBI tax ID(s): 546115 (species)
General
@ref: 17780
BacDive-ID: 7455
DSM-Number: 24823
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped
description: Microbacterium ginsengiterrae DSM 24823 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil of ginseng field.
NCBI tax id
- NCBI tax id: 546115
- Matching level: species
strain history
@ref | history |
---|---|
17780 | <- JCM <- <- D.-C. Yang; DCY37 |
67770 | D.-C. Yang DCY37. |
67771 | <- DC Yang, Kyunghee Univ. |
doi: 10.13145/bacdive7455.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Microbacterium
- species: Microbacterium ginsengiterrae
- full scientific name: Microbacterium ginsengiterrae Kim et al. 2010
@ref: 17780
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Microbacterium
species: Microbacterium ginsengiterrae
full scientific name: Microbacterium ginsengiterrae Kim et al. 2010
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29554 | positive | 1.5-2 µm | 0.5-0.7 µm | rod-shaped | no | |
67771 | positive | |||||
69480 | positive | 100 |
pigmentation
- @ref: 29554
- production: yes
Culture and growth conditions
culture medium
- @ref: 17780
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17780 | positive | growth | 28 | mesophilic |
29554 | positive | growth | 15-45 | |
29554 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29554 | positive | growth | 05-09 | alkaliphile |
29554 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29554 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
29554 | yes | |
69480 | no | 99.828 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29554 | NaCl | positive | growth | 01-08 % |
29554 | NaCl | positive | optimum | 01-08 % |
observation
@ref | observation |
---|---|
29554 | aggregates in chains |
67770 | quinones: MK-12, MK-13 |
67771 | quinones: MK-12 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29554 | 16193 | 3-hydroxybenzoate | + | carbon source |
29554 | 17879 | 4-hydroxybenzoate | + | carbon source |
29554 | 26546 | rhamnose | + | carbon source |
29554 | 33942 | ribose | + | carbon source |
29554 | 17992 | sucrose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29554 | catalase | + | 1.11.1.6 |
29554 | cytochrome oxidase | + | 1.9.3.1 |
29554 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
17780 | soil of ginseng field | Republic of Korea | KOR | Asia |
67770 | Soil of a ginseng field | Republic of Korea | KOR | Asia |
67771 | From soil, ginseng field | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Field |
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
Safety information
risk assessment
- @ref: 17780
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
29554 | Microbacterium ginsengiterrae strain DCY37 16S ribosomal RNA gene, partial sequence | EU873314.1 | 1427 | nuccore | 546115 |
17780 | Microbacterium ginsengiterrae strain DCY37 16S ribosomal RNA gene, partial sequence | EU873314 | 1427 | ena | 546115 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium ginsengiterrae DSM 24823 | GCA_014205075 | contig | ncbi | 546115 |
66792 | Microbacterium ginsengiterrae JCM 15516 | GCA_015278215 | contig | ncbi | 546115 |
66792 | Microbacterium ginsengiterrae strain DSM 24823 | 546115.4 | wgs | patric | 546115 |
66792 | Microbacterium ginsengiterrae strain JCM 15516 | 546115.5 | wgs | patric | 546115 |
66792 | Microbacterium ginsengiterrae DSM 24823 | 2870791180 | draft | img | 546115 |
GC content
@ref | GC-content | method |
---|---|---|
17780 | 64.5 | high performance liquid chromatography (HPLC) |
29554 | 64.5 | |
67771 | 64.54 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 89 | no |
gram-positive | yes | 96.322 | no |
anaerobic | no | 99.555 | yes |
halophile | no | 80.699 | no |
spore-forming | no | 85.544 | yes |
glucose-util | yes | 84.881 | no |
thermophile | no | 99.461 | yes |
aerobic | yes | 94.405 | no |
motile | no | 88.303 | no |
flagellated | no | 97.6 | yes |
glucose-ferment | no | 89.182 | no |
External links
@ref: 17780
culture collection no.: DSM 24823, JCM 15516, KCTC 19526, DCY 37, NBRC 110802
straininfo link
- @ref: 76902
- straininfo: 374135
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20081025 | Microbacterium ginsengiterrae sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field. | Kim YJ, Kim MK, Bui TPN, Kim HB, Srinivasan S, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.015784-0 | 2010 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry, beta-Glucosidase/metabolism | Genetics |
Phylogeny | 25678679 | Microbacterium shaanxiense sp. nov., isolated from the nodule surface of soybean. | Peng S, Dongying L, Bingxin Y, Mingjun L, Gehong W | Int J Syst Evol Microbiol | 10.1099/ijs.0.000116 | 2015 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Soybeans/*microbiology, Vitamin K 2/chemistry | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
17780 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24823) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24823 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
29554 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25949 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
76902 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID374135.1 | StrainInfo: A central database for resolving microbial strain identifiers |