Strain identifier
BacDive ID: 2378
Type strain:
Species: Oerskovia turbata
Strain Designation: 27, AB 1476, N32, Oerskov 27
Strain history: CIP <- 1983, H. Prauser, IMET, Oerskovia turbata <- H. Lautrop, Statens Serum Inst., Copenhagen, Denmark: strain Oerskov 27
NCBI tax ID(s): 1322249 (strain), 1713 (species)
General
@ref: 8927
BacDive-ID: 2378
DSM-Number: 20577
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive, human pathogen
description: Oerskovia turbata 27 is a mesophilic, Gram-positive human pathogen that was isolated from soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1322249 | strain |
1713 | species |
strain history
@ref | history |
---|---|
8927 | <- NCIB <- M. Goodfellow, N32 <- H. Lautrop, AB 1476 <- (J. Oerskov, 27) |
67770 | KCC A-0160 <-- IMRU 689 <-- Statens Serum Inst., Copenhagen, Denmark; 891 (Ørskov's strain 27). |
123692 | CIP <- 1983, H. Prauser, IMET, Oerskovia turbata <- H. Lautrop, Statens Serum Inst., Copenhagen, Denmark: strain Oerskov 27 |
doi: 10.13145/bacdive2378.20230509.8.1
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 turbata
- full scientific name: Oerskovia turbata (Erikson 1954) Prauser et al. 1970 (Approved Lists 1980)
synonyms
@ref synonym 20215 Cellulomonas turbata 20215 Nocardia turbata
@ref: 8927
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Promicromonosporaceae
genus: Oerskovia
species: Oerskovia turbata
full scientific name: Oerskovia turbata (Erikson 1954) Prauser et al. 1970 emend. Nouioui et al. 2018
strain designation: 27, AB 1476, N32, Oerskov 27
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
18449 | Beige (1001) | 10-14 days | ISP 2 |
18449 | Sulfur yellow (1016) | 10-14 days | ISP 3 |
18449 | Broom yellow (1032) | 10-14 days | ISP 4 |
18449 | Broom yellow (1032) | 10-14 days | ISP 5 |
18449 | Broom yellow (1032) | 10-14 days | ISP 6 |
18449 | Broom yellow (1032) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
18449 | no | ISP 2 |
18449 | no | ISP 3 |
18449 | no | ISP 4 |
18449 | no | ISP 5 |
18449 | no | ISP 6 |
18449 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8927 | CORYNEBACTERIUM AGAR (DSMZ Medium 53) | yes | https://mediadive.dsmz.de/medium/53 | Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water |
18449 | 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 | |
18449 | 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 | |
18449 | 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 | |
18449 | 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 | |
18449 | 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 | |
18449 | 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: | |
38084 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
37022 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
123692 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18449 | positive | optimum | 30 | mesophilic |
8927 | positive | growth | 30 | mesophilic |
38084 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.758
halophily
- @ref: 18449
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 7.5 %
murein
- @ref: 8927
- murein short key: A11.45
- type: A4alpha L-Lys-L-Thr-D-Asp
observation
- @ref: 67770
- observation: quinones: MK-9(H4), MK-9(II,III-H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18449 | 17234 | glucose | + | |
18449 | 22599 | arabinose | + | |
18449 | 17992 | sucrose | + | |
18449 | 18222 | xylose | - | |
18449 | 17268 | myo-inositol | - | |
18449 | 29864 | mannitol | - | |
18449 | 28757 | fructose | + | |
18449 | 26546 | rhamnose | - | |
18449 | 16634 | raffinose | - | |
18449 | 62968 | cellulose | - | |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
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 | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
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 | alpha-galactosidase | - | 3.2.1.22 |
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 lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
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 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | - | 3.2.1.23 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18449 | + | - | + | + | - | + | + | + | + | - | - | + | + | + | + | + | + | + | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18449 | + | + | + | - | + | + | - | - | - | + | + | - | + | - | + | + | + | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18449 | - | - | - | - | - | - | - | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | isolation date |
---|---|---|---|---|---|
8927 | soil | ||||
123692 | Environment, Soil | Denmark | DNK | Europe | 1938 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_702.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_493;98_564;99_702&stattab=map
- Last taxonomy: Oerskovia
- 16S sequence: X79454
- Sequence Identity:
- Total samples: 10823
- soil counts: 3597
- aquatic counts: 1485
- animal counts: 1997
- plant counts: 3744
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
8927 | yes, in single cases | 1 | Risk group (German classification) |
123692 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | C.turbata 16S rRNA gene | X83806 | 1451 | ena | 1322249 |
20218 | Oerskovia turbata NCIMB 10587 16S rDNA | X79454 | 1510 | ena | 1322249 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Oerskovia turbata strain JCM3160 | 1713.5 | wgs | patric | 1713 |
67770 | Oerskovia turbata NRRL B-8019 | GCA_000718325 | contig | ncbi | 1713 |
67770 | Oerskovia turbata JCM3160 | GCA_004121315 | contig | ncbi | 1713 |
GC content
@ref | GC-content | method |
---|---|---|
8927 | 70.5 | |
67770 | 72.2 | genome sequence analysis |
67770 | 72.3 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 81 | no |
motile | yes | 67.524 | no |
gram-positive | yes | 90.047 | no |
anaerobic | no | 98.982 | no |
aerobic | yes | 90.251 | no |
halophile | no | 92.798 | no |
spore-forming | no | 82.621 | no |
thermophile | no | 99.581 | no |
glucose-util | yes | 82.978 | no |
flagellated | no | 90.676 | no |
glucose-ferment | no | 68.684 | yes |
External links
@ref: 8927
culture collection no.: DSM 20577, ATCC 25835, CIP 100331, DSM 43880, JCM 3160, NCIB 10587, CCM 4093, CFBP 4266, CGMCC 4.1139, CIP 81.27, IAM 14867, IFM 10527, IFO 13506, IFO 15015, IMET 7405, IMSNU 21326, KCCM 12155, KCTC 9084, LMG 4072, NBRC 13506, NBRC 15015, NCIMB 10587, NCTC 11973, NRRL B-8019, RIA 1564, VKM Ac-1024, CCUG 17963
straininfo link
- @ref: 71933
- straininfo: 13609
literature
- topic: Phylogeny
- Pubmed-ID: 31980859
- title: Isolation, Substrate Specificity, and Subunit Characterization of the Xylanosomes Produced by Oerskovia turbata JCM 3160.
- authors: Dou TY, Liu WJ, Chen J
- journal: Curr Microbiol
- DOI: 10.1007/s00284-020-01887-7
- year: 2020
- mesh: Actinobacteria/classification/*enzymology/genetics/metabolism, Bacterial Proteins/*chemistry/genetics/isolation & purification/*metabolism, Genome, Bacterial/genetics, Molecular Weight, Multienzyme Complexes/chemistry/genetics/isolation & purification/metabolism, Phylogeny, Polysaccharides/metabolism, Protein Subunits/chemistry/genetics, Proteomics, Substrate Specificity, Xylans/metabolism
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8927 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20577) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20577 | |||
18449 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM20577.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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
37022 | Curators of the CIP | Collection of Institut Pasteur (CIP 81.27) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.27 | |||
38084 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/11784 | ||||
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/ | ||||
68368 | Automatically annotated from API 20E | |||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
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) | |||
71933 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13609.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123692 | Curators of the CIP | Collection of Institut Pasteur (CIP 100331) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20100331 |