Strain identifier
BacDive ID: 159622
Type strain: 
Species: Ruthenibacterium lactatiformans
Strain Designation: WCA3-601-WT-6J
Strain history: <- T. Clavel , TU Munich, Freising-Weihenstephan, Germany; WCA3-601-WT-6J
NCBI tax ID(s): 1550024 (species)
version 8.1 (current version)
General
@ref: 66457
BacDive-ID: 159622
DSM-Number: 105274
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Ruthenibacterium lactatiformans WCA3-601-WT-6J is a mesophilic bacterium that was isolated from pig, WT, 24 weeks old, feces.
NCBI tax id
- NCBI tax id: 1550024
- Matching level: species
strain history
- @ref: 66457
- history: <- T. Clavel , TU Munich, Freising-Weihenstephan, Germany; WCA3-601-WT-6J
doi: 10.13145/bacdive159622.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Ruthenibacterium
- species: Ruthenibacterium lactatiformans
- full scientific name: Ruthenibacterium lactatiformans Shkoporov et al. 2016
@ref: 66457
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Oscillospiraceae
genus: Ruthenibacterium
species: Ruthenibacterium lactatiformans
full scientific name: Ruthenibacterium lactatiformans Shkoporov et al. 2016
strain designation: WCA3-601-WT-6J
type strain: no
Culture and growth conditions
culture medium
- @ref: 66457
- name: CHOPPED MEAT MEDIUM (DSMZ Medium 78)
- growth: yes
- link: https://mediadive.dsmz.de/medium/78
- composition: Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
culture temp
- @ref: 66457
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68367 | 27082 | trehalose | - | builds acid from |
| 68367 | 62345 | L-rhamnose | - | builds acid from |
| 68367 | 30911 | sorbitol | - | builds acid from |
| 68367 | 16634 | raffinose | - | builds acid from |
| 68367 | 6731 | melezitose | - | builds acid from |
| 68367 | 16024 | D-mannose | - | builds acid from |
| 68367 | 17057 | cellobiose | - | builds acid from |
| 68367 | 17754 | glycerol | - | builds acid from |
| 68367 | 4853 | esculin | - | hydrolysis |
| 68367 | 5291 | gelatin | - | hydrolysis |
| 68367 | 30849 | L-arabinose | - | builds acid from |
| 68367 | 65327 | D-xylose | - | builds acid from |
| 68367 | 17814 | salicin | - | builds acid from |
| 68367 | 17306 | maltose | + | builds acid from |
| 68367 | 17992 | sucrose | - | builds acid from |
| 68367 | 17716 | lactose | - | builds acid from |
| 68367 | 16899 | D-mannitol | - | builds acid from |
| 68367 | 16199 | urea | - | hydrolysis |
| 68367 | 27897 | tryptophan | - | energy source |
metabolite production
- @ref: 68367
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68367
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68367 | beta-glucosidase | - | 3.2.1.21 |
| 68367 | gelatinase | - | |
| 68367 | urease | - | 3.5.1.5 |
API 20A
| @ref | IND | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 66457 | - | - | +/- | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 66457
- sample type: pig, WT, 24 weeks old, feces
- geographic location: Kranzberg (Bavaria)
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
| #Host | #Mammals | #Suidae (Pig,Swine) |
taxonmaps
- @ref: 69479
- File name: preview.99_3903.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_286;96_1997;97_2400;98_2967;99_3903&stattab=map
- Last taxonomy: Ruthenibacterium lactatiformans subclade
- 16S sequence: MN537483
- Sequence Identity:
- Total samples: 305547
- soil counts: 1989
- aquatic counts: 6411
- animal counts: 296291
- plant counts: 856
Safety information
risk assessment
- @ref: 66457
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 66457
- description: Ruthenibacterium lactatiformans strain DSM 105274 16S ribosomal RNA gene, partial sequence
- accession: MN537483
- length: 1483
- database: ena
- NCBI tax ID: 1550024
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Ruthenibacterium lactatiformans WCA3-601-WT-6J | GCA_009695715 | contig | ncbi | 1550024 |
| 66792 | Ruthenibacterium lactatiformans strain WCA3-601-WT-6J | 1550024.411 | wgs | patric | 1550024 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 93.42 | no |
| gram-positive | yes | 90.04 | no |
| anaerobic | yes | 98.902 | no |
| aerobic | no | 97.991 | no |
| halophile | no | 93.398 | no |
| spore-forming | no | 63.587 | no |
| thermophile | no | 97.738 | yes |
| glucose-util | yes | 88.766 | no |
| flagellated | no | 96.759 | no |
| glucose-ferment | yes | 74.936 | no |
External links
@ref: 66457
culture collection no.: DSM 105274
straininfo link
- @ref: 112096
- straininfo: 398287
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 66457 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-105274 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105274) | |
| 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 | |
| 68367 | Automatically annotated from API 20A | |||
| 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/ | |
| 112096 | 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-ID398287.1 |