Strain identifier
BacDive ID: 7447
Type strain:
Species: Microbacterium insulae
Strain Designation: DS-66
Strain history: <- JH Yoon, KRIBB
NCBI tax ID(s): 483014 (species)
General
@ref: 16654
BacDive-ID: 7447
DSM-Number: 23024
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped
description: Microbacterium insulae DS-66 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 483014
- Matching level: species
strain history
@ref | history |
---|---|
16654 | <- CCUG <- J.-H. Yoon, KRIBB |
67770 | CCUG 54523 <-- J.-H. Yoon DS-66. |
67771 | <- JH Yoon, KRIBB |
doi: 10.13145/bacdive7447.20230509.8.1
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 insulae
- full scientific name: Microbacterium insulae Yoon et al. 2009
@ref: 16654
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Microbacterium
species: Microbacterium insulae
full scientific name: Microbacterium insulae Yoon et al. 2009
strain designation: DS-66
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29157 | positive | 1.15 µm | 0.35 µm | coccus-shaped | no | |
67771 | positive | |||||
69480 | positive | 100 |
colony morphology
- @ref: 60213
- incubation period: 1-2 days
pigmentation
- @ref: 29157
- production: yes
Culture and growth conditions
culture medium
- @ref: 16654
- 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 | range |
---|---|---|---|---|
16654 | positive | growth | 28 | mesophilic |
29157 | positive | growth | 20-38 | |
29157 | positive | optimum | 30 | mesophilic |
60213 | positive | growth | 30-37 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29157 | positive | growth | 5.5-8.0 |
29157 | positive | optimum | 6.75 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
60213 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
29157 | no | |
69481 | no | 100 |
69480 | no | 99.987 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29157 | NaCl | positive | growth | 0-5 % |
29157 | NaCl | positive | optimum | 0.75 % |
murein
- @ref: 16654
- murein short key: B06
- type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn
observation
- @ref: 67770
- observation: quinones: MK-13, MK-12, MK-14
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29157 | 22599 | arabinose | + | carbon source |
29157 | 17057 | cellobiose | + | carbon source |
29157 | 28757 | fructose | + | carbon source |
29157 | 28260 | galactose | + | carbon source |
29157 | 5291 | gelatin | + | carbon source |
29157 | 17234 | glucose | + | carbon source |
29157 | 17754 | glycerol | + | carbon source |
29157 | 17716 | lactose | + | carbon source |
29157 | 17306 | maltose | + | carbon source |
29157 | 29864 | mannitol | + | carbon source |
29157 | 37684 | mannose | + | carbon source |
29157 | 37657 | methyl D-glucoside | + | carbon source |
29157 | 26546 | rhamnose | + | carbon source |
29157 | 17814 | salicin | + | carbon source |
29157 | 17992 | sucrose | + | carbon source |
29157 | 27082 | trehalose | + | carbon source |
29157 | 53424 | tween 20 | + | carbon source |
29157 | 53423 | tween 40 | + | carbon source |
29157 | 53425 | tween 60 | + | carbon source |
29157 | 53426 | tween 80 | + | carbon source |
29157 | 18222 | xylose | + | carbon source |
29157 | 4853 | esculin | + | hydrolysis |
enzymes
- @ref: 29157
- value: cytochrome oxidase
- activity: +
- ec: 1.9.3.1
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
16654 | soil | Dokdo | Republic of Korea | KOR | Asia | |
60213 | Soil | Dokdo | Republic of Korea | KOR | Asia | 2004-05-01 |
67770 | Soil | |||||
67771 | From soil | Dokdo | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 16654
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16654
- description: Microbacterium insulae strain DS-66 16S ribosomal RNA gene, partial sequence
- accession: EU239498
- length: 1447
- database: ena
- NCBI tax ID: 483014
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium insulae strain DSM 23024 | 483014.3 | wgs | patric | 483014 |
66792 | Microbacterium insulae DSM 23024 | 2893599951 | draft | img | 483014 |
GC content
@ref | GC-content | method |
---|---|---|
16654 | 69.9 | high performance liquid chromatography (HPLC) |
29157 | 69.9 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | yes | 92.08 | no |
anaerobic | no | 99.614 | yes |
halophile | no | 92.057 | no |
spore-forming | no | 91.244 | yes |
glucose-util | yes | 86.003 | yes |
aerobic | yes | 96.942 | yes |
thermophile | no | 99.109 | yes |
motile | no | 90.762 | yes |
flagellated | no | 97.527 | yes |
glucose-ferment | no | 90.235 | no |
External links
@ref: 16654
culture collection no.: DSM 23024, CCUG 54523, KCTC 19247, JCM 19115
straininfo link
- @ref: 76895
- straininfo: 407518
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19542140 | Microbacterium insulae sp. nov., isolated from soil. | Yoon JH, Schumann P, Kang SJ, Lee CS, Lee SY, Oh TK | Int J Syst Evol Microbiol | 10.1099/ijs.0.007591-0 | 2009 | Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Genes, rRNA, Genotype, Korea, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity | Genetics |
Phylogeny | 20656817 | Microbacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems. | Kampfer P, Rekha PD, Schumann P, Arun AB, Young CC, Chen WM, Sridhar KR | Int J Syst Evol Microbiol | 10.1099/ijs.0.026401-0 | 2010 | Actinomycetales/*classification/genetics/*isolation & purification, Amino Acids/analysis, Animals, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Feces/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis | Genetics |
Phylogeny | 22280899 | Microbacterium marinum sp. nov., isolated from deep-sea water. | Zhang L, Xi L, Ruan J, Huang Y | Syst Appl Microbiol | 10.1016/j.syapm.2011.11.004 | 2012 | Actinomycetales/*classification/*genetics/isolation & purification, Aquatic Organisms/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition/genetics, Base Sequence, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Indian Ocean, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Sequence Alignment, Sequence Analysis, DNA | Enzymology |
Phylogeny | 27506590 | Microbacterium aureliae sp. nov., a novel actinobacterium isolated from Aurelia aurita, the moon jellyfish. | Kaur G, Mual P, Kumar N, Verma A, Kumar A, Krishnamurthi S, Mayilraj S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001407 | 2016 | Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, India, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Scyphozoa/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16654 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23024) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23024 | |||
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 | |||
29157 | 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 | 25581 | 28776041 | |
60213 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 54523) | https://www.ccug.se/strain?id=54523 | |||
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) | |||
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) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
76895 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407518.1 | StrainInfo: A central database for resolving microbial strain identifiers |