Strain identifier
BacDive ID: 65
Type strain: 
Species: Stella vacuolata
Strain history: <- VKM
NCBI tax ID(s): 1123295 (strain), 217070 (species)
version 9.1 (current version)
General
@ref: 2353
BacDive-ID: 65
DSM-Number: 5901
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, chemoorganotroph, Gram-negative, star-shaped, colony-forming
description: Stella vacuolata DSM 5901 is a microaerophile, chemoorganotroph, Gram-negative bacterium that forms circular colonies and was isolated from horse manure and sewage sludge of a piggery.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 217070 | species |
| 1123295 | strain |
strain history
- @ref: 2353
- history: <- VKM
doi: 10.13145/bacdive65.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Stellaceae
- genus: Stella
- species: Stella vacuolata
- full scientific name: Stella vacuolata Vasilyeva 1985
@ref: 2353
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Stellaceae
genus: Stella
species: Stella vacuolata
full scientific name: Stella vacuolata Vasilyeva 1985
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell shape | motility | confidence |
|---|---|---|---|---|---|
| 23248 | negative | 1.9-2.5 µm | star-shaped | no | |
| 69480 | negative | 98.327 |
colony morphology
- @ref: 23248
- colony size: 2.5 mm
- colony color: milky white
- colony shape: circular
multimedia
- @ref: 2353
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_5901.jpg
- caption: Micrograph of DSM 5901. Scale bar represent 5 um.
- intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Culture and growth conditions
culture medium
- @ref: 2353
- name: ANCALOMICROBIUM MEDIUM (DSMZ Medium 603)
- growth: yes
- link: https://mediadive.dsmz.de/medium/603
- composition: Name: ANCALOMICROBIUM MEDIUM (DSMZ Medium 603) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.588119 g/l (NH4)2SO4 0.247525 g/l Glucose 0.247525 g/l Nitrilotriacetic acid 0.19802 g/l Na2HPO4 0.070297 g/l CaCl2 x 2 H2O 0.0660396 g/l ZnSO4 x 7 H2O 0.00108416 g/l FeSO4 x 7 H2O 0.00049505 g/l Na-EDTA 0.000247525 g/l (NH4)6Mo7O24 x 4 H2O 0.000183168 g/l MnSO4 x H2O 0.000152475 g/l Calcium pantothenate 4.95049e-05 g/l Nicotinamide 4.95049e-05 g/l Riboflavin 4.95049e-05 g/l Thiamine-HCl x 2 H2O 4.95049e-05 g/l CuSO4 x 5 H2O 3.88119e-05 g/l Co(NO3)2 x 6 H2O 2.45545e-05 g/l Biotin 1.9802e-05 g/l Folic acid 1.9802e-05 g/l Na2B4O7 x 10 H2O 1.75248e-05 g/l Vitamin B12 9.90099e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 2353 | positive | growth | 28 |
| 23248 | positive | optimum | 28 |
culture pH
- @ref: 23248
- ability: positive
- type: growth
- pH: 7
Physiology and metabolism
oxygen tolerance
- @ref: 23248
- oxygen tolerance: microaerophile
nutrition type
- @ref: 23248
- type: chemoorganotroph
spore formation
- @ref: 69481
- spore formation: no
- confidence: 95
halophily
- @ref: 23248
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 1 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23248 | 17968 | butyrate | - | growth |
| 23248 | 24265 | gluconate | - | growth |
| 23248 | 16467 | L-arginine | - | growth |
| 23248 | 29991 | L-aspartate | - | growth |
| 23248 | 15971 | L-histidine | - | growth |
| 23248 | 18019 | L-lysine | - | growth |
| 23248 | 17203 | L-proline | - | growth |
| 23248 | 17115 | L-serine | - | growth |
| 23248 | 26986 | threonine | - | growth |
| 23248 | 31011 | valerate | - | growth |
| 23248 | 62968 | cellulose | - | hydrolysis |
| 23248 | 5291 | gelatin | - | hydrolysis |
| 23248 | 28017 | starch | - | hydrolysis |
| 23248 | 30916 | 2-oxoglutarate | + | growth |
| 23248 | 30089 | acetate | + | growth |
| 23248 | 16947 | citrate | + | growth |
| 23248 | 15570 | D-alanine | + | growth |
| 23248 | 15740 | formate | + | growth |
| 23248 | 29806 | fumarate | + | growth |
| 23248 | 16977 | L-alanine | + | growth |
| 23248 | 17196 | L-asparagine | + | growth |
| 23248 | 17561 | L-cysteine | + | growth |
| 23248 | 16283 | L-cystine | + | growth |
| 23248 | 29985 | L-glutamate | + | growth |
| 23248 | 18050 | L-glutamine | + | growth |
| 23248 | 24996 | lactate | + | growth |
| 23248 | 25115 | malate | + | growth |
| 23248 | 15361 | pyruvate | + | growth |
| 23248 | 30031 | succinate | + | growth |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 23248 | horse manure and sewage sludge of a piggery | Leningrad region | Russia | RUS | Europe |
| 2353 | horse manure | Russia | RUS | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Waste | #Sewage sludge |
| #Host | #Mammals | #Equidae (Horse) |
| #Host | #Mammals | #Suidae (Pig,Swine) |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_141380.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_634;96_20993;97_26151;98_33233;99_141380&stattab=map
- Last taxonomy: Stella vacuolata
- 16S sequence: AJ535711
- Sequence Identity:
- Total samples: 136
- soil counts: 27
- aquatic counts: 90
- animal counts: 12
- plant counts: 7
Safety information
risk assessment
- @ref: 2353
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Stella vacuolata 16S rRNA gene, strain DSM5901
- accession: AJ535711
- length: 1447
- database: nuccore
- NCBI tax ID: 217070
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Stella vacuolata ATCC 43931 | GCA_006739055 | complete | ncbi | 217070 |
| 66792 | Stella vacuolata strain ATCC 43931 | 217070.3 | complete | patric | 217070 |
| 66792 | Stella vacuolata ATCC 43931 | 2883517513 | complete | img | 217070 |
GC content
- @ref: 23248
- GC-content: 73.50
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 95 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.327 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.203 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 73.671 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 82.189 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.053 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 65.176 | no |
External links
@ref: 2353
culture collection no.: DSM 5901, ATCC 43931, AUCM B-1552, BKM B-1552, DSM 3699, VKM B-1552
straininfo link
- @ref: 69749
- straininfo: 42131
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15143003 | Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the 'Alphaproteobacteria' and description of Angulomicrobium amanitiforme sp. nov. | Fritz I, Strompl C, Abraham WR | Int J Syst Evol Microbiol | 10.1099/ijs.0.02746-0 | 2004 | Acetobacteraceae/*classification/genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Hyphomicrobiaceae/*classification/genetics/metabolism, Lipids/analysis, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics | Metabolism |
| Genetics | 31395645 | Complete Genome Sequences of Three Star-Shaped Bacteria, Stella humosa, Stella vacuolata, and Stella Species ATCC 35155. | Shibai A, Maeda T, Kawada M, Kotani H, Sakata N, Furusawa C | Microbiol Resour Announc | 10.1128/MRA.00719-19 | 2019 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2353 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5901) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5901 | |||
| 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 | |
| 23248 | L. V. VASILYEVA | 10.1099/00207713-35-4-518 | Stella, a New Genus of Soil Prosthecobacteria, with Proposals for Stella humosa sp. nov. and Stella vacuolata sp. nov. | IJSEM 35: 518-521 1985 | ||
| 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) | |||
| 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 | |||
| 69749 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42131.1 | StrainInfo: A central database for resolving microbial strain identifiers |