Strain identifier
BacDive ID: 130284
Type strain: 
Species: Desulfoprunum benzoelyticum
Strain Designation: KoBa311
Strain history: <- M. Junghare, Dept. Biol., Univ. Konstanz, Germany; KoBa311 <- M. Junghare {2013}
NCBI tax ID(s): 1506996 (species)
version 9.3 (current version)
General
@ref: 22137
BacDive-ID: 130284
DSM-Number: 28570
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Desulfoprunum benzoelyticum KoBa311 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from sewage sludge from a municipal wastewater treatment plant.
NCBI tax id
- NCBI tax id: 1506996
- Matching level: species
strain history
- @ref: 22137
- history: <- M. Junghare, Dept. Biol., Univ. Konstanz, Germany; KoBa311 <- M. Junghare {2013}
doi: 10.13145/bacdive130284.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfobacterales
- family: Desulfobulbaceae
- genus: Desulfoprunum
- species: Desulfoprunum benzoelyticum
- full scientific name: Desulfoprunum benzoelyticum Junghare and Schink 2015
@ref: 22137
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfobacterales
family: Desulfobulbaceae
genus: Desulfoprunum
species: Desulfoprunum benzoelyticum
full scientific name: Desulfoprunum benzoelyticum Junghare and Schink 2015
strain designation: KoBa311
type strain: yes
Morphology
cell morphology
- @ref: 125438
- gram stain: negative
- confidence: 95.229
colony morphology
- @ref: 22137
- incubation period: 8-14 days
Culture and growth conditions
culture medium
- @ref: 22137
- 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; with strain-specific modifications) Composition: Na2SO4 2.99103 g/l Na2CO3 1.49551 g/l NaCl 0.997009 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l MgCl2 x 6 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l Na-benzoate 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 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 (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l p-Aminobenzoic acid 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: 22137
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 22137 | anaerobe | |
| 125439 | anaerobe | 98.2 |
Isolation, sampling and environmental information
isolation
- @ref: 22137
- sample type: sewage sludge from a municipal wastewater treatment plant
- geographic location: Konstanz
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Waste | #Sewage sludge |
| #Engineered | #Waste | #Water treatment plant |
Safety information
risk assessment
- @ref: 22137
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22137
- description: Desulfoprunum benzoelyticum strain KoBa311 16S ribosomal RNA gene, partial sequence
- accession: KJ766003
- length: 1357
- database: nuccore
- NCBI tax ID: 1506996
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfoprunum benzoelyticum DSM 28570 | GCA_014201505 | scaffold | ncbi | 1506996 |
| 66792 | Desulfoprunum benzoelyticum DSM 28570 | GCA_016918515 | contig | ncbi | 1506996 |
| 66792 | Desulfoprunum benzoelyticum strain DSM 28570 | 1506996.4 | wgs | patric | 1506996 |
| 66792 | Desulfoprunum benzoelyticum strain DSM 28570 | 1506996.3 | wgs | patric | 1506996 |
| 66792 | Desulfoprunum benzoelyticum DSM 28570 | 2861203348 | draft | img | 1506996 |
GC content
- @ref: 22137
- GC-content: 52.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 95.229 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 76.583 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 79.346 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 85.053 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 87.939 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 50.799 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 87.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 64.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 85.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 98.2 |
External links
@ref: 22137
culture collection no.: DSM 28570, KCTC 15441
straininfo link
- @ref: 88819
- straininfo: 404777
literature
- topic: Phylogeny
- Pubmed-ID: 25278560
- title: Desulfoprunum benzoelyticum gen. nov., sp. nov., a Gram-stain-negative, benzoate-degrading, sulfate-reducing bacterium isolated from a wastewater treatment plant.
- authors: Junghare M, Schink B
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.066761-0
- year: 2014
- mesh: Base Composition, Benzoates/*metabolism, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Germany, Molecular Sequence Data, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sulfates/*metabolism, Vitamin K 2/chemistry
- 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 | |
| 22137 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28570 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28570) | |
| 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 | |
| 88819 | 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-ID404777.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |