Strain identifier

BacDive ID: 2382

Type strain: Yes

Species: Oerskovia jenensis

Strain Designation: 377-78

Strain history: CIP <- 1983, IMET, Cellulomonas turbata <- H. Prauser: strain 377-78 Oerskovia turbata

NCBI tax ID(s): 162169 (species)

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General

@ref: 12274

BacDive-ID: 2382

DSM-Number: 46000

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped

description: Oerskovia jenensis 377-78 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil, coniferous wood.

NCBI tax id

  • NCBI tax id: 162169
  • Matching level: species

strain history

@refhistory
12274<- IMET <- H. Prauser, 377-78 (Oerskovia turbata)
67770DSM 46000 <-- IMET 7006 <-- H. Prauser 377-78.
120335CIP <- 1983, IMET, Cellulomonas turbata <- H. Prauser: strain 377-78 Oerskovia turbata

doi: 10.13145/bacdive2382.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Oerskovia
  • species: Oerskovia jenensis
  • full scientific name: Oerskovia jenensis Stackebrandt et al. 2002

@ref: 12274

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Oerskovia

species: Oerskovia jenensis

full scientific name: Oerskovia jenensis Stackebrandt et al. 2002

strain designation: 377-78

type strain: yes

Morphology

cell morphology

  • @ref: 120335
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
20188Colorless10-14 daysISP 2
20188Colorless10-14 daysISP 3
20188Beige (1001)10-14 daysISP 4
20188Beige (1001)10-14 daysISP 5
20188Beige (1001)10-14 daysISP 6
20188Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20188noISP 2
20188noISP 3
20188noISP 4
20188noISP 5
20188noISP 6
20188noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12274TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
20188ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20188ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20188ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20188ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20188ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20188ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
40733MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120335CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120335CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
20188positiveoptimum28
12274positivegrowth28
40733positivegrowth30
57535positivegrowth26-37
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57535aerobe
120335facultative anaerobe

murein

  • @ref: 12274
  • murein short key: A11.57
  • type: A4alpha L-Lys-L-Thr-D-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2018817234glucose-
2018822599arabinose-
2018817992sucrose-
2018818222xylose-
2018817268myo-inositol-
2018829864mannitol-
2018828757fructose+
2018826546rhamnose-
2018816634raffinose-
2018862968cellulose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol+builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12033517632nitrate+reduction
12033516301nitrite-reduction
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

metabolite production

  • @ref: 120335
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
120335oxidase-
120335catalase+1.11.1.6
120335urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    57535C14:03.814
    57535C15:00.815
    57535C16:06.716
    57535C15:0 ANTEISO62.114.711
    57535C15:0 ISO13.214.621
    57535C15:1 ANTEISO A0.814.526
    57535C16:0 iso2.615.626
    57535C17:0 anteiso8.116.722
    57535C17:0 iso0.616.629
    57535C18:2 ω6,9c/C18:0 ANTE1.417.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20188+-++-++++--+++-+-++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20188+++-++---++++-+++--
120335-+--++---++-+-+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120335+/----++-+--++/-+-------+++/-+++++/-+-++---++-++------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationsampling datecountrycontinentorigin.countryisolation date
12274soil, coniferous woodCarpathian Mountains
57535Soil,spruce-forestCarpathian Mountains1978CzechoslovakiaEurope
67770Soil
120335Environment, SoilCzech RepublicEuropeCZE1978

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil
#Host#Plants#Tree

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
122741Risk group (German classification)
201881
1203351Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12274
  • description: Oerskovia jenensis 16S rRNA gene, strain DSM 46000
  • accession: AJ314848
  • length: 1484
  • database: nuccore
  • NCBI tax ID: 162169

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oerskovia jenensis DSM 46000GCA_016907235contigncbi162169
66792Oerskovia jenensis strain DSM 46000162169.4wgspatric162169
66792Oerskovia jenensis DSM 460002892702859draftimg162169

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes68no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.139no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.085yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes50.576no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes74.346no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.9yes
69480flagellatedmotile2+Ability to perform flagellated movementno66.5no

External links

@ref: 12274

culture collection no.: DSM 46000, CIP 100330, IMET 7006, CCUG 47142, JCM 9969, CCM 4094, IFO 15012, LMG 16191, NBRC 15012

straininfo link

  • @ref: 71937
  • straininfo: 7898

phages

  • @ref: 124042
  • name: Oerskovia phage O3
  • strain number: DSM 46000
  • link: https://phagedive.dsmz.de/strain/741

literature

  • topic: Phylogeny
  • Pubmed-ID: 12148614
  • title: Re-evaluation of the status of the genus Oerskovia, reclassification of Promicromonospora enterophila (Jager et al. 1983) as Oerskovia enterophila comb. nov. and description of Oerskovia jenensis sp. nov. and Oerskovia paurometabola sp. nov.
  • authors: Stackebrandt E, Breymann S, Steiner U, Prauser H, Weiss N, Schumann P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-4-1105
  • year: 2002
  • mesh: Actinomycetales/chemistry/*classification/genetics, Bacterial Typing Techniques, Cellulomonas/chemistry/classification/genetics, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
12274Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46000)https://www.dsmz.de/collection/catalogue/details/culture/DSM-46000
20188Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM46000.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
40733Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11783
57535Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47142)https://www.ccug.se/strain?id=47142
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71937Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7898.1StrainInfo: A central database for resolving microbial strain identifiers
120335Curators of the CIPCollection of Institut Pasteur (CIP 100330)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20100330
124042Dr. Johannes Wittmann, Dr. Clara Rolland, Dr. Lorenz Reimer, Joaquim Sardàhttps://phagedive.dsmz.de/PhageDive