Strain identifier
BacDive ID: 2382
Type strain:
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)
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
@ref | history |
---|---|
12274 | <- IMET <- H. Prauser, 377-78 (Oerskovia turbata) |
67770 | DSM 46000 <-- IMET 7006 <-- H. Prauser 377-78. |
120335 | CIP <- 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
@ref | colony color | incubation period | medium used |
---|---|---|---|
20188 | Colorless | 10-14 days | ISP 2 |
20188 | Colorless | 10-14 days | ISP 3 |
20188 | Beige (1001) | 10-14 days | ISP 4 |
20188 | Beige (1001) | 10-14 days | ISP 5 |
20188 | Beige (1001) | 10-14 days | ISP 6 |
20188 | Beige (1001) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
20188 | no | ISP 2 |
20188 | no | ISP 3 |
20188 | no | ISP 4 |
20188 | no | ISP 5 |
20188 | no | ISP 6 |
20188 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12274 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: 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 |
20188 | ISP 2 | yes | Name: 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 | |
20188 | ISP 3 | yes | Name: 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: | |
20188 | ISP 4 | yes | Name: 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 | |
20188 | ISP 5 | yes | Name: 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 | |
20188 | ISP 6 | yes | Name: 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 | |
20188 | ISP 7 | yes | Name: 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 | |
40733 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
120335 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
120335 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature |
---|---|---|---|
20188 | positive | optimum | 28 |
12274 | positive | growth | 28 |
40733 | positive | growth | 30 |
57535 | positive | growth | 26-37 |
67770 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
57535 | aerobe |
120335 | facultative 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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
20188 | 17234 | glucose | - | |
20188 | 22599 | arabinose | - | |
20188 | 17992 | sucrose | - | |
20188 | 18222 | xylose | - | |
20188 | 17268 | myo-inositol | - | |
20188 | 29864 | mannitol | - | |
20188 | 28757 | fructose | + | |
20188 | 26546 | rhamnose | - | |
20188 | 16634 | raffinose | - | |
20188 | 62968 | cellulose | + | |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | + | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | + | builds acid from |
68371 | 28066 | gentiobiose | + | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | + | builds acid from |
68371 | 28017 | starch | + | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | + | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | + | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 17814 | salicin | + | builds acid from |
68371 | 4853 | esculin | + | builds acid from |
68371 | 18305 | arbutin | + | builds acid from |
68371 | 59640 | N-acetylglucosamine | + | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | + | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | + | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | + | builds acid from |
68371 | 16988 | D-ribose | + | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
120335 | 17632 | nitrate | + | reduction |
120335 | 16301 | nitrite | - | reduction |
68379 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | + | fermentation |
68379 | 16988 | D-ribose | + | fermentation |
68379 | 65327 | D-xylose | + | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | + | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | + | fermentation |
68379 | 28087 | glycogen | + | fermentation |
metabolite production
- @ref: 120335
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase (C 4) | + | |
68379 | gelatinase | - | |
68379 | urease | - | 3.5.1.5 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
120335 | oxidase | - | |
120335 | catalase | + | 1.11.1.6 |
120335 | urease | - | 3.5.1.5 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 57535 C14:0 3.8 14 57535 C15:0 0.8 15 57535 C16:0 6.7 16 57535 C15:0 ANTEISO 62.1 14.711 57535 C15:0 ISO 13.2 14.621 57535 C15:1 ANTEISO A 0.8 14.526 57535 C16:0 iso 2.6 15.626 57535 C17:0 anteiso 8.1 16.722 57535 C17:0 iso 0.6 16.629 57535 C18:2 ω6,9c/C18:0 ANTE 1.4 17.724 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20188 | + | - | + | + | - | + | + | + | + | - | - | + | + | + | - | + | - | + | + |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20188 | + | + | + | - | + | + | - | - | - | + | + | + | + | - | + | + | + | - | - | |
120335 | - | + | - | - | + | + | - | - | - | + | + | - | + | - | + | + | + | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120335 | +/- | - | - | - | + | + | - | + | - | - | + | +/- | + | - | - | - | - | - | - | - | + | + | +/- | + | + | + | + | +/- | + | - | + | + | - | - | - | + | + | - | + | + | - | - | - | - | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | sampling date | country | continent | origin.country | isolation date |
---|---|---|---|---|---|---|---|
12274 | soil, coniferous wood | Carpathian Mountains | |||||
57535 | Soil,spruce-forest | Carpathian Mountains | 1978 | Czechoslovakia | Europe | ||
67770 | Soil | ||||||
120335 | Environment, Soil | Czech Republic | Europe | CZE | 1978 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Forest |
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Tree |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
12274 | 1 | Risk group (German classification) |
20188 | 1 | |
120335 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Oerskovia jenensis DSM 46000 | GCA_016907235 | contig | ncbi | 162169 |
66792 | Oerskovia jenensis strain DSM 46000 | 162169.4 | wgs | patric | 162169 |
66792 | Oerskovia jenensis DSM 46000 | 2892702859 | draft | img | 162169 |
Genome-based predictions
predictions
@ref | trait | model | description | prediction | confidence | training_data |
---|---|---|---|---|---|---|
69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 68 | no |
69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 89.139 | no |
69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.085 | yes |
69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 50.576 | no |
69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 74.346 | no |
69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 96.9 | yes |
69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 66.5 | no |
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
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
12274 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46000) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-46000 | |
20188 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM46000.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |
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 | |
40733 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/11783 | ||
57535 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 47142) | https://www.ccug.se/strain?id=47142 | |
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) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68371 | Automatically annotated from API 50CH acid | |||
68379 | Automatically annotated from API Coryne | |||
68382 | Automatically annotated from API zym | |||
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 | |
71937 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID7898.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
120335 | Curators of the CIP | Collection of Institut Pasteur (CIP 100330) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20100330 | |
124042 | Dr. Johannes Wittmann, Dr. Clara Rolland, Dr. Lorenz Reimer, Joaquim Sardà | https://phagedive.dsmz.de/ | PhageDive |