Strain identifier
BacDive ID: 7472
Type strain: 
Species: Okibacterium fritillariae
Strain history: NBRC 16404 <-- IFO 16404 <-- L. I. Evtushenko VKM Ac-2059.
NCBI tax ID(s): 123320 (species)
version 8.1 (current version)
General
@ref: 5787
BacDive-ID: 7472
DSM-Number: 15271
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Okibacterium fritillariae DSM 15271 is a mesophilic bacterium that was isolated from seeds of Fritellaria ruthenica Wikstr..
NCBI tax id
- NCBI tax id: 123320
- Matching level: species
strain history
| @ref | history |
|---|---|
| 5787 | <- IFO; IFO 16404 |
| 67770 | NBRC 16404 <-- IFO 16404 <-- L. I. Evtushenko VKM Ac-2059. |
doi: 10.13145/bacdive7472.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Okibacterium
- species: Okibacterium fritillariae
- full scientific name: Okibacterium fritillariae Evtushenko et al. 2002
@ref: 5787
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Okibacterium
species: Okibacterium fritillariae
full scientific name: Okibacterium fritillariae Evtushenko et al. 2002
type strain: yes
Culture and growth conditions
culture medium
- @ref: 5787
- 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 |
|---|---|---|---|---|
| 5787 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-10, MK-11
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 5787 | seeds of Fritellaria ruthenica Wikstr. | Fritellaria ruthenica | Prioksko-Terrasny Biospere Park, Moscow region | Russia | RUS | Europe |
| 67770 | Seed of Fritillaria ruthenica in Prioksko-Terrasny Biosphere Park | Fritillaria ruthenica | Moscow Region | Russia | RUS |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Fruit (Seed) |
taxonmaps
- @ref: 69479
- File name: preview.99_4185.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_895;97_1924;98_3157;99_4185&stattab=map
- Last taxonomy: Okibacterium fritillariae subclade
- 16S sequence: AM410675
- Sequence Identity:
- Total samples: 3283
- soil counts: 702
- aquatic counts: 367
- animal counts: 1505
- plant counts: 709
Safety information
risk assessment
- @ref: 5787
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Okibacterium fritillariae partial 16S rRNA gene, type strain DSM 15271 | AM410675 | 1506 | ena | 123320 |
| 5787 | Curtobacterium sp. VKM Ac-2059 gene for 16S ribosomal RNA, partial sequence | AB042094 | 1506 | ena | 123320 |
Genome sequences
- @ref: 67770
- description: Okibacterium fritillariae VKM Ac-2059
- accession: GCA_900167575
- assembly level: contig
- database: ncbi
- NCBI tax ID: 123320
GC content
| @ref | GC-content | method |
|---|---|---|
| 5787 | 67 | |
| 67770 | 66.6 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 91.657 | no |
| flagellated | no | 98.022 | no |
| gram-positive | yes | 95.181 | no |
| anaerobic | no | 99.562 | no |
| aerobic | yes | 92.352 | no |
| halophile | no | 89.692 | no |
| spore-forming | no | 90.889 | no |
| thermophile | no | 99.312 | yes |
| glucose-util | yes | 86.917 | no |
| glucose-ferment | no | 91.12 | no |
External links
@ref: 5787
culture collection no.: DSM 15271, IFO 16404, NBRC 16404, VKM AC-2059, JCM 12284, IAM 15090
straininfo link
- @ref: 76917
- straininfo: 62353
literature
- topic: Phylogeny
- Pubmed-ID: 12054268
- title: Okibacterium fritillariae gen. nov., sp. nov., a novel genus of the family Microbacteriaceae.
- authors: Evtushenko LI, Dorofeeva LV, Krausova VI, Gavrish EY, Yashina SG, Takeuchi M
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-52-3-987
- year: 2002
- mesh: Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Clematis/*microbiology, DNA, Ribosomal/analysis, Fritillaria/*microbiology, Molecular Sequence Data, Peptidoglycan/analysis/chemistry, Phospholipids, RNA, Ribosomal, 16S/genetics, Seeds/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analysis
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5787 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15271) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15271 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 76917 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID62353.1 | StrainInfo: A central database for resolving microbial strain identifiers |