Strain identifier
BacDive ID: 13907
Type strain:
Species: Sterolibacterium denitrificans
Strain Designation: Chol-1S
Strain history: <- S. Tarlera; chol1
NCBI tax ID(s): 157592 (species)
General
@ref: 5211
BacDive-ID: 13907
DSM-Number: 13999
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic
description: Sterolibacterium denitrificans Chol-1S is an aerobe, mesophilic bacterium that was isolated from denitrifying reactor treating sanitary landfill leakate.
NCBI tax id
- NCBI tax id: 157592
- Matching level: species
strain history
- @ref: 5211
- history: <- S. Tarlera; chol1
doi: 10.13145/bacdive13907.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Nitrosomonadales
- family: Sterolibacteriaceae
- genus: Sterolibacterium
- species: Sterolibacterium denitrificans
- full scientific name: Sterolibacterium denitrificans Tarlera and Denner 2003
@ref: 5211
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Rhizobiales
family: Sterolibacteriaceae
genus: Sterolibacterium
species: Sterolibacterium denitrificans
full scientific name: Sterolibacterium denitrificans Tarlera and Denner 2003
strain designation: Chol-1S
type strain: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5211 | ANAEROBIC CHOLESTEROL MEDIUM (DSMZ Medium 858) | yes | https://mediadive.dsmz.de/medium/858 | Name: ANAEROBIC CHOLESTEROL MEDIUM (DSMZ Medium 858) Composition: NaHCO3 4.2 g/l NaNO3 0.72 g/l KH2PO4 0.5 g/l NH4Cl 0.45 g/l MgSO4 x 7 H2O 0.45 g/l CaCl2 0.09 g/l HCl 0.00625 g/l FeCl2 x 4 H2O 0.00375 g/l NaOH 0.00125 g/l CoCl2 x 6 H2O 0.000475 g/l Riboflavin 0.00025 g/l alpha-lipoic acid 0.00025 g/l p-Aminobenzoic acid 0.00025 g/l Thiamine-HCl x 2 H2O 0.00025 g/l Pantothenic acid 0.00025 g/l Vitamin B12 0.00025 g/l MnCl2 x 4 H2O 0.00025 g/l ZnCl2 0.000175 g/l Nicotine amide 0.000125 g/l Nicotinic acid 0.000125 g/l Folic acid 0.0001 g/l Biotin 0.0001 g/l Na2MoO4 x 2 H2O 9e-05 g/l NiCl2 x 6 H2O 6e-05 g/l Pyridoxamine hydrochloride 5e-05 g/l H3BO3 1.5e-05 g/l Na2WO4 x 2 H2O 1e-05 g/l Na2SeO3 x 5 H2O 7.5e-06 g/l CuCl2 x 2 H2O 5e-06 g/l Distilled water |
5211 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
culture temp
- @ref: 5211
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
5211 | aerobe |
5211 | anaerobe |
compound production
- @ref: 5211
- compound: ethylbenzene dehydrogenase
Isolation, sampling and environmental information
isolation
- @ref: 5211
- sample type: denitrifying reactor treating sanitary landfill leakate
- geographic location: Montevideo
- country: Uruguay
- origin.country: URY
- continent: Middle and South America
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Bioreactor | |
#Engineered | #Waste | #Landfill |
#Engineered | #Waste | #Wastewater |
Safety information
risk assessment
- @ref: 5211
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5211
- description: Sterolibacterium denitrificans 16S rRNA gene, strain Chol-1S
- accession: AJ306683
- length: 1531
- database: ena
- NCBI tax ID: 157592
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Sterolibacterium denitrificans DSM 13999 | GCA_001586935 | scaffold | ncbi | 157592 |
66792 | Sterolibacterium denitrificans strain DSM 13999 | 157592.11 | wgs | patric | 157592 |
66792 | Sterolibacterium denitrificans DSM 13999 | 2690315849 | draft | img | 157592 |
GC content
- @ref: 5211
- GC-content: 65.3
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 73.342 | no |
gram-positive | no | 98.219 | no |
anaerobic | no | 66.327 | no |
aerobic | no | 72.482 | no |
halophile | no | 90.191 | no |
spore-forming | no | 97.097 | no |
glucose-util | no | 50 | no |
motile | yes | 89.741 | no |
thermophile | no | 92.137 | yes |
glucose-ferment | no | 71.358 | no |
External links
@ref: 5211
culture collection no.: DSM 13999, ATCC BAA 354, Chol chol1, Chol 1
straininfo link
- @ref: 83082
- straininfo: 113529
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12892131 | Sterolibacterium denitrificans gen. nov., sp. nov., a novel cholesterol-oxidizing, denitrifying member of the beta-Proteobacteria. | Tarlera S, Denner EBM | Int J Syst Evol Microbiol | 10.1099/ijs.0.02039-0 | 2003 | Base Composition, Base Sequence, Betaproteobacteria/*classification/genetics/isolation & purification/*metabolism, Cholesterol/*metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Microscopy, Electron, Molecular Sequence Data, Nitrates/metabolism, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Uruguay | Metabolism |
Metabolism | 16825628 | Denitratisoma oestradiolicum gen. nov., sp. nov., a 17beta-oestradiol-degrading, denitrifying betaproteobacterium. | Fahrbach M, Kuever J, Meinke R, Kampfer P, Hollender J | Int J Syst Evol Microbiol | 10.1099/ijs.0.63672-0 | 2006 | Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification/*metabolism, Biodegradation, Environmental, Carbohydrate Metabolism, Carbon Dioxide/metabolism, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Estradiol/*metabolism, Fatty Acids/chemistry/metabolism, Genes, rRNA, Molecular Sequence Data, Movement, Nitrogen/*metabolism, Oxidoreductases/analysis, Phylogeny, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Spores, Bacterial, Water/metabolism, Water Microbiology | Phylogeny |
Metabolism | 18039763 | Study of anoxic and oxic cholesterol metabolism by Sterolibacterium denitrificans. | Chiang YR, Ismail W, Heintz D, Schaeffer C, Van Dorsselaer A, Fuchs G | J Bacteriol | 10.1128/JB.01525-07 | 2007 | Aerobiosis, Anaerobiosis, Cholesterol/*metabolism, Cosmids, Escherichia coli/enzymology/genetics, Gene Library, Isomerases/genetics/isolation & purification/*metabolism, Molecular Sequence Data, Oxidoreductases/genetics/isolation & purification/*metabolism, Rhodocyclaceae/*enzymology/genetics/*growth & development/metabolism, Sequence Analysis, DNA | Enzymology |
Phylogeny | 19799633 | A strictly anaerobic betaproteobacterium Georgfuchsia toluolica gen. nov., sp. nov. degrades aromatic compounds with Fe(III), Mn(IV) or nitrate as an electron acceptor. | Weelink SA, van Doesburg W, Saia FT, Rijpstra WI, Roling WF, Smidt H, Stams AJ | FEMS Microbiol Ecol | 10.1111/j.1574-6941.2009.00778.x | 2009 | Betaproteobacteria/*classification/genetics/growth & development/metabolism, Biodegradation, Environmental, Carbon-Carbon Lyases/genetics, DNA, Bacterial/genetics, Ferric Compounds/*metabolism, Fresh Water/microbiology, Netherlands, Nitrates/*metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Toluene/metabolism, Water Microbiology | Metabolism |
Metabolism | 27726023 | Regioselective hydroxylation of cholecalciferol, cholesterol and other sterol derivatives by steroid C25 dehydrogenase. | Rugor A, Tataruch M, Staron J, Dudzik A, Niedzialkowska E, Nowak P, Hogendorf A, Michalik-Zym A, Napruszewska DB, Jarzebski A, Szymanska K, Bialas W, Szaleniec M | Appl Microbiol Biotechnol | 10.1007/s00253-016-7880-2 | 2016 | Betaproteobacteria/enzymology, Biocatalysis, Bioreactors, Calcifediol/metabolism, Cholecalciferol/*metabolism, Cholesterol/*metabolism, Hydroxycholesterols/metabolism, Hydroxylation, Metabolic Engineering, Oxidoreductases/chemistry/*isolation & purification/*metabolism, Sterols/*metabolism | Enzymology |
Enzymology | 28343996 | Optimization of overexpression of a chaperone protein of steroid C25 dehydrogenase for biochemical and biophysical characterization. | Niedzialkowska E, Mrugala B, Rugor A, Czub MP, Skotnicka A, Cotelesage JJH, George GN, Szaleniec M, Minor W, Lewinski K | Protein Expr Purif | 10.1016/j.pep.2017.03.019 | 2017 | *Bacterial Proteins/biosynthesis/chemistry/genetics/isolation & purification, *Coenzymes/biosynthesis/chemistry/genetics/isolation & purification, Escherichia coli/chemistry/genetics/*metabolism, *Gene Expression, *Metalloproteins/biosynthesis/chemistry/genetics/isolation & purification, *Molecular Chaperones/biosynthesis/chemistry/genetics/isolation & purification, Molybdenum Cofactors, Nitrosomonadaceae/*genetics/metabolism, *Pteridines/chemistry/isolation & purification, Recombinant Proteins/biosynthesis/chemistry/genetics/isolation & purification | Phylogeny |
Enzymology | 28482186 | Reaction mechanism of sterol hydroxylation by steroid C25 dehydrogenase - Homology model, reactivity and isoenzymatic diversity. | Rugor A, Wojcik-Augustyn A, Niedzialkowska E, Mordalski S, Staron J, Bojarski A, Szaleniec M | J Inorg Biochem | 10.1016/j.jinorgbio.2017.04.027 | 2017 | Anaerobiosis, Catalytic Domain, Gram-Negative Bacteria/enzymology, Hydrogen Bonding, Hydroxylation, Hydroxysteroids/metabolism, Isoenzymes/chemistry/*metabolism, Ketosteroids/metabolism, Kinetics, Oxidoreductases/chemistry/*metabolism, Rhodocyclaceae/enzymology, Substrate Specificity | Metabolism |
Metabolism | 30680854 | The 7alpha-hydroxysteroid dehydratase Hsh2 is essential for anaerobic degradation of the steroid skeleton of 7alpha-hydroxyl bile salts in the novel denitrifying bacterium Azoarcus sp. strain Aa7. | Yucel O, Borgert SR, Poehlein A, Niermann K, Philipp B | Environ Microbiol | 10.1111/1462-2920.14508 | 2019 | Anaerobiosis, Azoarcus/enzymology/genetics/*metabolism, Bacterial Proteins/genetics/*metabolism, Bile Acids and Salts/chemistry/*metabolism, Cholates/metabolism, Denitrification, Hydroxysteroid Dehydrogenases/genetics/*metabolism, Hydroxysteroids/metabolism, Rhodocyclaceae/enzymology/genetics/metabolism, Steroids/chemistry/metabolism | Enzymology |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
5211 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13999) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13999 | |
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) | |
83082 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID113529.1 | StrainInfo: A central database for resolving microbial strain identifiers |