Strain identifier
BacDive ID: 4004
Type strain: 
Species: Desulfobulbus propionicus
Strain history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; Lindhorst (1pr3) <- F. Widdel {1976}
NCBI tax ID(s): 577650 (strain), 894 (species)
version 9.1 (current version)
General
@ref: 677
BacDive-ID: 4004
DSM-Number: 2032
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative
description: Desulfobulbus propionicus DSM 2032 is an anaerobe, Gram-negative bacterium that was isolated from freshwater mud.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 894 | species |
| 577650 | strain |
strain history
- @ref: 677
- history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; Lindhorst (1pr3) <- F. Widdel {1976}
doi: 10.13145/bacdive4004.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfobacterales
- family: Desulfobulbaceae
- genus: Desulfobulbus
- species: Desulfobulbus propionicus
- full scientific name: Desulfobulbus propionicus Widdel 1981
synonyms
- @ref: 20215
- synonym: Desulfobulbus propionicus
@ref: 677
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfobacterales
family: Desulfobulbaceae
genus: Desulfobulbus
species: Desulfobulbus propionicus
full scientific name: Desulfobulbus propionicus Widdel 1981
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 98.067
multimedia
- @ref: 66793
- multimedia content: EM_DSM_2032_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 677
- name: DESULFOBULBUS SP. MEDIUM (FRESHWATER) (DSMZ Medium 194)
- growth: yes
- link: https://mediadive.dsmz.de/medium/194
- composition: Name: DESULFOBULBUS SP. MEDIUM (FRESHWATER) (DSMZ Medium 194) Composition: Na2SO4 2.99103 g/l Na2CO3 1.49551 g/l Na-propionate 1.49551 g/l NaCl 0.997009 g/l KCl 0.498504 g/l MgCl2 x 6 H2O 0.398804 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
- @ref: 677
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
- @ref: 677
- oxygen tolerance: anaerobe
spore formation
- @ref: 69481
- spore formation: no
- confidence: 96
Isolation, sampling and environmental information
isolation
- @ref: 677
- sample type: freshwater mud
- geographic location: Hannover, Lindhorst
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Terrestrial | #Mud (Sludge) |
taxonmaps
- @ref: 69479
- File name: preview.99_6115.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_128;96_380;97_3581;98_4535;99_6115&stattab=map
- Last taxonomy: Desulfobulbus propionicus subclade
- 16S sequence: AY548789
- Sequence Identity:
- Total samples: 1987
- soil counts: 235
- aquatic counts: 1593
- animal counts: 57
- plant counts: 102
Safety information
risk assessment
- @ref: 677
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | D.propionicus 16S ribosomal rRNA | M34410 | 1371 | nuccore | 894 |
| 677 | Desulfobulbus propionicus 16S ribosomal RNA gene gene, partial sequence | AY548789 | 1533 | nuccore | 577650 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfobulbus propionicus DSM 2032 | GCA_000186885 | complete | ncbi | 577650 |
| 66792 | Desulfobulbus propionicus DSM 2032 | 577650.3 | complete | patric | 577650 |
| 66792 | Desulfobulbus propionicus 1pr3, DSM 2032 | 649633036 | complete | img | 577650 |
GC content
- @ref: 677
- GC-content: 59.9
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 96 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.067 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 85.772 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 84.49 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 85.577 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 91.04 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 72.048 | no |
External links
@ref: 677
culture collection no.: DSM 2032, ATCC 33891, Lindhorst (1pr3)
straininfo link
- @ref: 73509
- straininfo: 40748
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 23115036 | Identification and characterization of the first cholesterol-dependent cytolysins from Gram-negative bacteria. | Hotze EM, Le HM, Sieber JR, Bruxvoort C, McInerney MJ, Tweten RK | Infect Immun | 10.1128/IAI.00927-12 | 2012 | Amino Acid Sequence, Cholesterol/*metabolism, Cytotoxins/*genetics/*metabolism, Gram-Negative Bacteria/*genetics/*metabolism, Molecular Sequence Data, Protein Binding/genetics, Proteobacteria/genetics/metabolism, RNA, Messenger/genetics | Genetics |
| Phylogeny | 27902225 | Desulfobulbus oligotrophicus sp. nov., a sulfate-reducing and propionate-oxidizing bacterium isolated from a municipal anaerobic sewage sludge digester. | El Houari A, Ranchou-Peyruse M, Ranchou-Peyruse A, Dakdaki A, Guignard M, Idouhammou L, Bennisse R, Bouterfass R, Guyoneaud R, Qatibi AI | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001615 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Morocco, Oxidation-Reduction, *Phylogeny, Propionates/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sulfur-Reducing Bacteria/classification/genetics/isolation & purification | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 677 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2032) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2032 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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 | |||
| 73509 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID40748.1 | StrainInfo: A central database for resolving microbial strain identifiers |