Strain identifier
BacDive ID: 24540
Type strain: 
Species: Rubrobacter aplysinae
Strain history: CECT 8425 <-- U. R. Abdelmosen; Univ. Würzburg, Germany; RV113.
NCBI tax ID(s): 909625 (species)
version 8.1 (current version)
General
@ref: 20789
BacDive-ID: 24540
DSM-Number: 27440
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Rubrobacter aplysinae DSM 27440 is a spore-forming, mesophilic bacterium that was isolated from Mediterranean sponge Aplysina aerophoba.
NCBI tax id
- NCBI tax id: 909625
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20789 | <- U. R. Abdelmosen, Univ. Würzburg; RV113 |
| 67770 | CECT 8425 <-- U. R. Abdelmosen; Univ. Würzburg, Germany; RV113. |
doi: 10.13145/bacdive24540.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Rubrobacteria
- order: Rubrobacterales
- family: Rubrobacteraceae
- genus: Rubrobacter
- species: Rubrobacter aplysinae
- full scientific name: Rubrobacter aplysinae Kämpfer et al. 2014
@ref: 20789
domain: Bacteria
phylum: Actinobacteria
class: Rubrobacteria
order: Rubrobacterales
family: Rubrobacteraceae
genus: Rubrobacter
species: Rubrobacter aplysinae
full scientific name: Rubrobacter aplysinae Kämpfer et al. 2014 emend. Nouioui et al. 2018
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 94.101 | |
| 69480 | 99.72 | positive |
Culture and growth conditions
culture medium
- @ref: 20789
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 19.45 g/l Starch 10.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20789 | positive | growth | 25 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | no | 99.24 |
observation
- @ref: 67770
- observation: quinones: MK-8, MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 20789 | Mediterranean sponge Aplysina aerophoba | Aplysina aerophoba | Rovinj | Croatia | HRV | Europe |
| 67770 | Sponge Aplysina aerophoba | Aplysina aerophoba | close to Rovinj | Croatia | HRV | Europe |
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Porifera (Sponges)
taxonmaps
- @ref: 69479
- File name: preview.99_4390.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_408;96_2197;97_2659;98_3296;99_4390&stattab=map
- Last taxonomy: Rubrobacter aplysinae subclade
- 16S sequence: GU318365
- Sequence Identity:
- Total samples: 989
- soil counts: 663
- aquatic counts: 124
- animal counts: 161
- plant counts: 41
Safety information
risk assessment
- @ref: 20789
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20789
- description: Rubrobacter aplysinae strain RV113 from Croatia 16S ribosomal RNA gene, partial sequence
- accession: GU318365
- length: 1512
- database: ena
- NCBI tax ID: 909625
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rubrobacter aplysinae strain RV113 | 909625.5 | wgs | patric | 909625 |
| 66792 | Rubrobacter aplysinae RV113 | 2867637810 | draft | img | 909625 |
| 67770 | Rubrobacter aplysinae RV113 | GCA_001029505 | scaffold | ncbi | 909625 |
GC content
- @ref: 67770
- GC-content: 65.1
- method: genome sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 85.196 | no |
| flagellated | no | 98.852 | no |
| gram-positive | yes | 73.683 | no |
| anaerobic | no | 93.008 | no |
| halophile | yes | 77.361 | no |
| spore-forming | no | 90.355 | no |
| thermophile | yes | 53.909 | yes |
| glucose-util | yes | 89.953 | no |
| aerobic | yes | 92.026 | no |
| glucose-ferment | no | 80.712 | no |
External links
@ref: 20789
culture collection no.: DSM 27440, CECT 8425, RV 113, JCM 31709
straininfo link
- @ref: 88395
- straininfo: 392960
literature
- topic: Phylogeny
- Pubmed-ID: 24170773
- title: Rubrobacter aplysinae sp. nov., isolated from the marine sponge Aplysina aerophoba.
- authors: Kampfer P, Glaeser SP, Busse HJ, Abdelmohsen UR, Hentschel U
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.055152-0
- year: 2013
- mesh: Actinobacteria/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lysine/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
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 | |
| 20789 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27440 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27440) | |
| 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 | |
| 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. | 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 | |
| 88395 | 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-ID392960.1 |