Strain identifier

BacDive ID: 13907

Type strain: Yes

Species: Sterolibacterium denitrificans

Strain Designation: Chol-1S

Strain history: <- S. Tarlera; chol1

NCBI tax ID(s): 157592 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

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

@refnamegrowthlinkcomposition
5211ANAEROBIC CHOLESTEROL MEDIUM (DSMZ Medium 858)yeshttps://mediadive.dsmz.de/medium/858Name: 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
5211R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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

@refoxygen tolerance
5211aerobe
5211anaerobe

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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sterolibacterium denitrificans DSM 13999GCA_001586935scaffoldncbi157592
66792Sterolibacterium denitrificans strain DSM 13999157592.11wgspatric157592
66792Sterolibacterium denitrificans DSM 139992690315849draftimg157592

GC content

  • @ref: 5211
  • GC-content: 65.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno73.342no
gram-positiveno98.219no
anaerobicno66.327no
aerobicno72.482no
halophileno90.191no
spore-formingno97.097no
glucose-utilno50no
motileyes89.741no
thermophileno92.137yes
glucose-fermentno71.358no

External links

@ref: 5211

culture collection no.: DSM 13999, ATCC BAA 354, Chol chol1, Chol 1

straininfo link

  • @ref: 83082
  • straininfo: 113529

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12892131Sterolibacterium denitrificans gen. nov., sp. nov., a novel cholesterol-oxidizing, denitrifying member of the beta-Proteobacteria.Tarlera S, Denner EBMInt J Syst Evol Microbiol10.1099/ijs.0.02039-02003Base 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, UruguayMetabolism
Metabolism16825628Denitratisoma oestradiolicum gen. nov., sp. nov., a 17beta-oestradiol-degrading, denitrifying betaproteobacterium.Fahrbach M, Kuever J, Meinke R, Kampfer P, Hollender JInt J Syst Evol Microbiol10.1099/ijs.0.63672-02006Base 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 MicrobiologyPhylogeny
Metabolism18039763Study of anoxic and oxic cholesterol metabolism by Sterolibacterium denitrificans.Chiang YR, Ismail W, Heintz D, Schaeffer C, Van Dorsselaer A, Fuchs GJ Bacteriol10.1128/JB.01525-072007Aerobiosis, 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, DNAEnzymology
Phylogeny19799633A 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 AJFEMS Microbiol Ecol10.1111/j.1574-6941.2009.00778.x2009Betaproteobacteria/*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 MicrobiologyMetabolism
Metabolism27726023Regioselective 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 MAppl Microbiol Biotechnol10.1007/s00253-016-7880-22016Betaproteobacteria/enzymology, Biocatalysis, Bioreactors, Calcifediol/metabolism, Cholecalciferol/*metabolism, Cholesterol/*metabolism, Hydroxycholesterols/metabolism, Hydroxylation, Metabolic Engineering, Oxidoreductases/chemistry/*isolation & purification/*metabolism, Sterols/*metabolismEnzymology
Enzymology28343996Optimization 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 KProtein Expr Purif10.1016/j.pep.2017.03.0192017*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 & purificationPhylogeny
Enzymology28482186Reaction 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 MJ Inorg Biochem10.1016/j.jinorgbio.2017.04.0272017Anaerobiosis, Catalytic Domain, Gram-Negative Bacteria/enzymology, Hydrogen Bonding, Hydroxylation, Hydroxysteroids/metabolism, Isoenzymes/chemistry/*metabolism, Ketosteroids/metabolism, Kinetics, Oxidoreductases/chemistry/*metabolism, Rhodocyclaceae/enzymology, Substrate SpecificityMetabolism
Metabolism30680854The 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 BEnviron Microbiol10.1111/1462-2920.145082019Anaerobiosis, 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/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitle
5211Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13999)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13999
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
83082Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID113529.1StrainInfo: A central database for resolving microbial strain identifiers