Strain identifier
BacDive ID: 130838
Type strain: 
Species: Labilithrix luteola
Strain Designation: B00002
Strain history: <- E. Yamamoto, Astellas Res. Technol. Co. Ltd., Ibaraki, Japan; B00002
NCBI tax ID(s): 1391654 (species)
version 9.1 (current version)
General
@ref: 22116
BacDive-ID: 130838
DSM-Number: 27648
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Labilithrix luteola B00002 is a Gram-negative bacterium that was isolated from forest soil.
NCBI tax id
- NCBI tax id: 1391654
- Matching level: species
strain history
- @ref: 22116
- history: <- E. Yamamoto, Astellas Res. Technol. Co. Ltd., Ibaraki, Japan; B00002
doi: 10.13145/bacdive130838.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Myxococcales
- family: Labilitrichaceae
- genus: Labilithrix
- species: Labilithrix luteola
- full scientific name: Labilithrix luteola Yamamoto et al. 2014
@ref: 22116
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Myxococcales
family: Labilitrichaceae
genus: Labilithrix
species: Labilithrix luteola
full scientific name: Labilithrix luteola Yamamoto et al. 2014
strain designation: B00002
type strain: yes
Morphology
multimedia
- @ref: 22116
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27648.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 22116 | NB-PYRUVATE AGAR (DSMZ Medium 1509) | yes | https://mediadive.dsmz.de/medium/1509 | Name: NB-PYRUVATE AGAR (DSMZ Medium 1509) Composition: Agar 14.0 g/l Nutrient broth 6.0 g/l NaCl 1.5 g/l Na-pyruvate 1.0 g/l Distilled water |
| 22116 | VY/2 AGAR (DSMZ Medium 9) | yes | https://mediadive.dsmz.de/medium/9 | Name: VY/2 AGAR (DSMZ Medium 9) Composition: Agar 15.0 g/l Baker's yeast 5.0 g/l CaCl2 x 2 H2O 1.36 g/l Vitamin B12 0.0005 g/l Distilled water |
| 22116 | CY-AGAR (DSMZ Medium 67) | yes | https://mediadive.dsmz.de/medium/67 | Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water |
culture temp
- @ref: 22116
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 96
Isolation, sampling and environmental information
isolation
- @ref: 22116
- sample type: forest soil
- geographic location: Kagoshima Prefecture, Yakushima Island
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Forest |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_87736.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_400;96_10573;97_46282;98_60630;99_87736&stattab=map
- Last taxonomy: Labilithrix luteola subclade
- 16S sequence: AB847449
- Sequence Identity:
- Total samples: 1000
- soil counts: 845
- aquatic counts: 35
- animal counts: 55
- plant counts: 65
Safety information
risk assessment
- @ref: 22116
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22116
- description: Labilithrix luteola gene for 16S ribosomal RNA, partial sequence
- accession: AB847449
- length: 1483
- database: nuccore
- NCBI tax ID: 1391654
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Labilithrix luteola DSM 27648 | GCA_001263205 | complete | ncbi | 1391654 |
| 66792 | Labilithrix luteola strain DSM 27648 | 1391654.11 | complete | patric | 1391654 |
| 66792 | Labilithrix luteola DSM 27648 | 2645727571 | complete | img | 1391654 |
GC content
- @ref: 22116
- GC-content: 66.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 96 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 87.432 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 86.19 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 77.025 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 70.571 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 98.412 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 64.421 | no |
External links
@ref: 22116
culture collection no.: DSM 27648, NBRC 109946
straininfo link
- @ref: 89325
- straininfo: 404660
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25048208 | Vulgatibacter incomptus gen. nov., sp. nov. and Labilithrix luteola gen. nov., sp. nov., two myxobacteria isolated from soil in Yakushima Island, and the description of Vulgatibacteraceae fam. nov., Labilitrichaceae fam. nov. and Anaeromyxobacteraceae fam. nov. | Yamamoto E, Muramatsu H, Nagai K | Int J Syst Evol Microbiol | 10.1099/ijs.0.063198-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Islands, Japan, Molecular Sequence Data, Myxococcales/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Metabolism | 29495640 | Six Heterocyclic Metabolites from the Myxobacterium Labilithrix luteola. | Mulwa LS, Jansen R, Praditya DF, Mohr KI, Wink J, Steinmann E, Stadler M | Molecules | 10.3390/molecules23030542 | 2018 | Anti-Infective Agents/chemistry/pharmacology, Antiviral Agents/chemistry/pharmacology, Biological Products/*chemistry/pharmacology, Fermentation, Hepacivirus/drug effects, Heterocyclic Compounds/*chemistry/pharmacology, Magnetic Resonance Spectroscopy, Microbial Sensitivity Tests, Molecular Structure, Myxococcales/*chemistry/metabolism, Secondary Metabolism | Pathogenicity |
Reference
| @id | authors | title | doi/url | catalogue | journal | 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 | |||
| 22116 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27648 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27648) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 89325 | 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-ID404660.1 |