Strain identifier
BacDive ID: 23031
Type strain: 
Species: Geomobilimonas luticola
Strain Designation: OSK6
Strain history: K. Nakamura OSK6.
NCBI tax ID(s): 1114878 (species)
version 8.1 (current version)
General
@ref: 19247
BacDive-ID: 23031
DSM-Number: 24905
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Geomobilimonas luticola OSK6 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from mud from lotus field.
NCBI tax id
- NCBI tax id: 1114878
- Matching level: species
strain history
| @ref | history |
|---|---|
| 19247 | <- K. Nakamura, Faculty Applied Biological Sci., Gifu Univ., Japan; OSK6 <- K. Nakamura {2011} |
| 67770 | K. Nakamura OSK6. |
doi: 10.13145/bacdive23031.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfuromonadales
- family: Geobacteraceae
- genus: Geomobilimonas
- species: Geomobilimonas luticola
- full scientific name: Geomobilimonas luticola (Viulu et al. 2013) Xu et al. 2022
synonyms
- @ref: 20215
- synonym: Geobacter luticola
@ref: 19247
domain: Bacteria
phylum: Pseudomonadota
class: Deltaproteobacteria
order: Desulfuromonadales
family: Geobacteraceae
genus: Geomobilimonas
species: Geomobilimonas luticola
full scientific name: Geomobilimonas luticola
strain designation: OSK6
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30588 | negative | 1.25 µm | 0.3 µm | rod-shaped | yes | |
| 69480 | negative | 99.999 |
pigmentation
- @ref: 30588
- production: yes
Culture and growth conditions
culture medium
- @ref: 19247
- name: GEOANAEROBACTER MEDIUM (DSMZ Medium 838)
- growth: yes
- link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium838.pdf
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 19247 | positive | growth | 30 | mesophilic |
| 30588 | positive | growth | 20-40 | |
| 30588 | positive | optimum | 33.5 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 30588 | positive | growth | 6.5-7.5 |
| 30588 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 19247 | anaerobe | |
| 30588 | anaerobe | |
| 69480 | anaerobe | 98.176 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.971 |
observation
- @ref: 67770
- observation: quinones: MK-8
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30588 | 30089 | acetate | + | carbon source |
| 30588 | 24996 | lactate | + | carbon source |
| 30588 | 15361 | pyruvate | + | carbon source |
| 30588 | 30031 | succinate | + | carbon source |
| 30588 | 17632 | nitrate | + | reduction |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 19247 | mud from lotus field | Aichi Prefecture, Aisai | Japan | JPN | Asia |
| 67770 | Lotus field mud in Aichi | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Host | #Plants | #Aquatic plant |
taxonmaps
- @ref: 69479
- File name: preview.99_173010.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15357;96_14329;97_17470;98_21696;99_173010&stattab=map
- Last taxonomy: Geobacter luticola subclade
- 16S sequence: AB682759
- Sequence Identity:
- Total samples: 116
- soil counts: 66
- aquatic counts: 44
- animal counts: 2
- plant counts: 4
Safety information
risk assessment
- @ref: 19247
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19247
- description: Geobacter luticola gene for 16S rRNA, partial sequence
- accession: AB682759
- length: 1478
- database: ena
- NCBI tax ID: 1114878
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geomobilimonas luticola JCM 17780 | GCA_018476905 | contig | ncbi | 1114878 |
| 66792 | Geobacter luticola strain JCM 17780 | 1114878.3 | wgs | patric | 1114878 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 19247 | 59.7 | high performance liquid chromatography (HPLC) |
| 30588 | 59.7 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 80.15 | no |
| flagellated | no | 95.483 | no |
| gram-positive | no | 98.82 | yes |
| anaerobic | yes | 96.018 | yes |
| aerobic | no | 96.35 | yes |
| halophile | no | 94.038 | no |
| spore-forming | no | 91.25 | no |
| thermophile | no | 94.834 | yes |
| glucose-util | no | 59.146 | no |
| glucose-ferment | no | 90.828 | no |
External links
@ref: 19247
culture collection no.: DSM 24905, JCM 17780
straininfo link
- @ref: 87271
- straininfo: 402242
literature
- topic: Phylogeny
- Pubmed-ID: 22493170
- title: Geobacter luticola sp. nov., an Fe(III)-reducing bacterium isolated from lotus field mud.
- authors: Viulu S, Nakamura K, Okada Y, Saitou S, Takamizawa K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.039321-0
- year: 2012
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Ferric Compounds/*metabolism, Geobacter/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Japan, Lotus/*microbiology, Molecular Sequence Data, Nitrates/metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 19247 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24905) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24905 | |||
| 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 | |||
| 30588 | 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 | 26919 | 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) | |||
| 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 | |||
| 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 | |||
| 87271 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402242.1 | StrainInfo: A central database for resolving microbial strain identifiers |