Strain identifier
BacDive ID: 132524
Type strain: 
Species: Risungbinella massiliensis
Strain Designation: GD1
Strain history: <- G. Dubourg, Hopital de la Timone,Marseille, France; GD1
NCBI tax ID(s): 1329796 (species)
version 8.1 (current version)
General
@ref: 24313
BacDive-ID: 132524
DSM-Number: 46691
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive
description: Risungbinella massiliensis GD1 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from feces of 38-year-old male who suffered from Coxiella burnetii vascular infection.
NCBI tax id
- NCBI tax id: 1329796
- Matching level: species
strain history
- @ref: 24313
- history: <- G. Dubourg, Hopital de la Timone,Marseille, France; GD1
doi: 10.13145/bacdive132524.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Thermoactinomycetaceae
- genus: Risungbinella
- species: Risungbinella massiliensis
- full scientific name: Risungbinella massiliensis Dubourg et al. 2016
@ref: 24313
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Thermoactinomycetaceae
genus: Risungbinella
species: Risungbinella massiliensis
full scientific name: Risungbinella massiliensis Dubourg et al. 2016
strain designation: GD1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
multimedia
- @ref: 24313
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_46691.jpg
- caption: Medium 535a 37°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 24313 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf | |
| 24313 | TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) | yes | https://mediadive.dsmz.de/medium/535a | Name: TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) Composition: None 50.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
culture temp
- @ref: 24313
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 24313
- sample type: feces of 38-year-old male who suffered from Coxiella burnetii vascular infection
- host species: Coxiella burnetii
- country: France
- origin.country: FRA
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Patient | |
| #Host | #Microbial | #Bacteria |
| #Host Body-Site | #Organ | #Vascular system |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
| #Host | #Human | #Male |
taxonmaps
- @ref: 69479
- File name: preview.99_2012.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_284;96_1117;97_1310;98_1576;99_2012&stattab=map
- Last taxonomy: Risungbinella massiliensis
- 16S sequence: HF952921
- Sequence Identity:
- Total samples: 3508
- soil counts: 857
- aquatic counts: 236
- animal counts: 2168
- plant counts: 247
Safety information
risk assessment
- @ref: 24313
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24313
- description: Thermoactinomycetaceae bacterium GD1 partial 16S rRNA gene, isolate GD1
- accession: HF952921
- length: 1464
- database: ena
- NCBI tax ID: 1329796
Genome sequences
- @ref: 66792
- description: Risungbinella massiliensis GD1
- accession: GCA_000942395
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 1329796
GC content
- @ref: 24313
- GC-content: 40.1
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 84.095 | no |
| flagellated | no | 92.739 | no |
| gram-positive | yes | 88.354 | no |
| anaerobic | no | 96.559 | no |
| aerobic | yes | 82.335 | no |
| halophile | no | 77.974 | no |
| spore-forming | yes | 93.02 | no |
| glucose-util | yes | 90.962 | no |
| thermophile | yes | 55.005 | no |
| glucose-ferment | no | 89.778 | no |
External links
@ref: 24313
culture collection no.: DSM 46691, CSUR P1082
straininfo link
- @ref: 90850
- straininfo: 402178
literature
- topic: Phylogeny
- Pubmed-ID: 26984352
- title: Risungbinella massiliensis sp. nov., a new member of Thermoactinomycetaceae isolated from human gut.
- authors: Dubourg G, Lagier JC, Robert C, Armstrong N, Couderc C, Fournier PE, Raoult D
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-016-0677-6
- year: 2016
- mesh: Adult, Bacillales/*classification/genetics/*isolation & purification/metabolism, Base Composition, Chromosome Mapping, DNA, Bacterial/genetics, Fatty Acids/metabolism, Genes, rRNA, Humans, Intestines/*microbiology, Male, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- topic2: Metabolism
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 | |
| 24313 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-46691 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46691) | |
| 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 | |
| 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 | |
| 90850 | 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-ID402178.1 |