Strain identifier
BacDive ID: 3817
Type strain: 
Species: Runella limosa
Strain Designation: EMB111
Strain history: <- CO Jeon, Gyungsang Univ.
NCBI tax ID(s): 1123077 (strain), 370978 (species)
version 8.1 (current version)
General
@ref: 7305
BacDive-ID: 3817
DSM-Number: 17973
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, rod-shaped
description: Runella limosa EMB111 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from activated sludge.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1123077 | strain |
| 370978 | species |
strain history
| @ref | history |
|---|---|
| 7305 | <- C. O. Jeon; EMB111 |
| 67771 | <- CO Jeon, Gyungsang Univ. |
doi: 10.13145/bacdive3817.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Spirosomataceae
- genus: Runella
- species: Runella limosa
- full scientific name: Runella limosa Ryu et al. 2006
@ref: 7305
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Spirosomaceae
genus: Runella
species: Runella limosa
full scientific name: Runella limosa Ryu et al. 2006 emend. Hahnke et al. 2016
strain designation: EMB111
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|
| 67771 | rod-shaped | no | ||
| 67771 | negative | |||
| 69480 | no | 94.596 | ||
| 69480 | negative | 99.998 |
Culture and growth conditions
culture medium
- @ref: 7305
- 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 |
|---|---|---|---|---|
| 7305 | positive | growth | 25 | mesophilic |
| 67771 | positive | growth | 25-30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.806 |
observation
- @ref: 67771
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 7305 | activated sludge | Pohang | Republic of Korea | KOR | Asia |
| 67771 | From activated sludge | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Activated sludge
taxonmaps
- @ref: 69479
- File name: preview.99_5339.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_516;96_2585;97_3167;98_3979;99_5339&stattab=map
- Last taxonomy: Runella limosa subclade
- 16S sequence: NR_043771
- Sequence Identity:
- Total samples: 2644
- soil counts: 71
- aquatic counts: 1191
- animal counts: 1354
- plant counts: 28
Safety information
risk assessment
- @ref: 7305
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Runella limosa strain EMB111 16S ribosomal RNA gene, partial sequence | DQ372985 | 1428 | ena | 370978 |
| 7305 | Runella limosa strain EMB111 16S ribosomal RNA, partial sequence | NR_043771 | 1428 | nuccore | 370978 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Runella limosa DSM 17973 | GCA_000482465 | scaffold | ncbi | 1123077 |
| 66792 | Runella limosa DSM 17973 | 1123077.3 | wgs | patric | 1123077 |
| 66792 | Runella limosa DSM 17973 | 2527291724 | draft | img | 1123077 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 7305 | 44.3 | sequence analysis |
| 67771 | 42.7 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 91.931 | yes |
| flagellated | no | 96.792 | yes |
| gram-positive | no | 97.557 | yes |
| anaerobic | no | 99.22 | yes |
| aerobic | yes | 86.692 | yes |
| halophile | no | 96.741 | no |
| spore-forming | no | 94.311 | no |
| thermophile | no | 98.343 | no |
| glucose-util | yes | 85.495 | no |
| glucose-ferment | no | 88.847 | no |
External links
@ref: 7305
culture collection no.: DSM 17973, KCTC 12615
straininfo link
- @ref: 73328
- straininfo: 297319
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17158973 | Runella limosa sp. nov., isolated from activated sludge. | Ryu SH, Nguyen TTH, Park W, Kim CJ, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.64460-0 | 2006 | Bacterial Typing Techniques, Cytophagaceae/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phosphorus/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology | Genetics |
| Phylogeny | 17978225 | Runella defluvii sp. nov., isolated from a domestic wastewater treatment plant. | Lu S, Lee JR, Ryu SH, Chung BS, Choe WS, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.65252-0 | 2007 | Bacterial Typing Techniques, Cytophagaceae/chemistry/*classification/genetics/*isolation & purification, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology, *Water Purification | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 7305 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17973) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17973 | |||
| 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 | |
| 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) | |||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | |||
| 73328 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297319.1 | StrainInfo: A central database for resolving microbial strain identifiers |