Strain identifier
BacDive ID: 3978
Type strain:
Species: Desulfobacula phenolica
Strain Designation: PhO1
Strain history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; PhO1 <- F. Bak {1984}
NCBI tax ID(s): 90732 (species)
General
@ref: 1370
BacDive-ID: 3978
DSM-Number: 3384
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Desulfobacula phenolica PhO1 is an anaerobe, mesophilic, motile bacterium that was isolated from marine mud.
NCBI tax id
- NCBI tax id: 90732
- Matching level: species
strain history
- @ref: 1370
- history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; PhO1 <- F. Bak {1984}
doi: 10.13145/bacdive3978.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfobacterales
- family: Desulfobacteraceae
- genus: Desulfobacula
- species: Desulfobacula phenolica
- full scientific name: Desulfobacula phenolica (Bak and Widdel 1988) Kuever et al. 2001
synonyms
- @ref: 20215
- synonym: Desulfobacterium phenolicum
@ref: 1370
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfobacterales
family: Desulfobacteraceae
genus: Desulfobacula
species: Desulfobacula phenolica
full scientific name: Desulfobacula phenolica (Bak and Widdel 1988) Kuever et al. 2001
strain designation: PhO1
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 95.953 | |
69480 | 99.999 | negative |
colony morphology
- @ref: 1370
- incubation period: 8-14 days
Culture and growth conditions
culture medium
- @ref: 1370
- name: DESULFOBACTERIUM MEDIUM (DSMZ Medium 383)
- growth: yes
- link: https://mediadive.dsmz.de/medium/383
- composition: Name: DESULFOBACTERIUM MEDIUM (DSMZ Medium 383; with strain-specific modifications) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na2CO3 0.997009 g/l KCl 0.498504 g/l Na-benzoate 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 Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 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: 1370
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
1370 | anaerobe | |
69480 | anaerobe | 98.65 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.896 |
Isolation, sampling and environmental information
isolation
- @ref: 1370
- sample type: marine mud
- geographic location: Venice
- country: Italy
- origin.country: ITA
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Terrestrial | #Mud (Sludge) |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_56160.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_40;96_82;97_86;98_95;99_56160&stattab=map
- Last taxonomy: Desulfobacula
- 16S sequence: AJ237606
- Sequence Identity:
- Total samples: 257
- soil counts: 5
- aquatic counts: 251
- plant counts: 1
Safety information
risk assessment
- @ref: 1370
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 1370
- description: Desulfobacterium phenolicum 16S rRNA gene, partial, strain DSM 3384
- accession: AJ237606
- length: 1508
- database: ena
- NCBI tax ID: 90732
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Desulfobacula phenolica DSM 3384 | GCA_900105645 | scaffold | ncbi | 90732 |
66792 | Desulfobacula phenolica strain DSM 3384 | 90732.5 | wgs | patric | 90732 |
66792 | Desulfobacula phenolica DSM 3384 | 2616644807 | draft | img | 90732 |
GC content
- @ref: 1370
- GC-content: 40.6
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
glucose-ferment | no | 85.951 | no |
flagellated | no | 61.598 | no |
gram-positive | no | 98.978 | no |
anaerobic | yes | 97.961 | yes |
aerobic | no | 97.399 | no |
halophile | no | 64.194 | no |
spore-forming | no | 87.351 | no |
thermophile | no | 96.776 | yes |
glucose-util | no | 58.174 | no |
motile | yes | 82.515 | no |
External links
@ref: 1370
culture collection no.: DSM 3384, ATCC 43956
straininfo link
- @ref: 73484
- straininfo: 42148
literature
- topic: Phylogeny
- Pubmed-ID: 22659505
- title: Desulfoconvexum algidum gen. nov., sp. nov., a psychrophilic sulfate-reducing bacterium isolated from a permanently cold marine sediment.
- authors: Konneke M, Kuever J, Galushko A, Jorgensen BB
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.043703-0
- year: 2012
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfur-Reducing Bacteria/*classification/genetics/isolation & purification, Svalbard
- topic2: Enzymology
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
1370 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3384) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3384 | |
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 | |
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 | |
73484 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42148.1 | StrainInfo: A central database for resolving microbial strain identifiers |