Strain identifier

BacDive ID: 11237

Type strain: Yes

Species: Nocardiopsis potens

Strain history: <- A. F. Yassin; IMMIB L-21

NCBI tax ID(s): 570268 (strain), 1246458 (species)

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General

@ref: 15894

BacDive-ID: 11237

DSM-Number: 45234

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, coccus-shaped

description: Nocardiopsis potens DSM 45234 is an aerobe, spore-forming, mesophilic bacterium that was isolated from household waste.

NCBI tax id

NCBI tax idMatching level
1246458species
570268strain

strain history

  • @ref: 15894
  • history: <- A. F. Yassin; IMMIB L-21

doi: 10.13145/bacdive11237.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis potens
  • full scientific name: Nocardiopsis potens Yassin et al. 2009

@ref: 15894

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis potens

full scientific name: Nocardiopsis potens Yassin et al. 2009 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29345positivecoccus-shapedno
29393positiveno
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19926Silver grey10-14 daysISP 2
19926Broom yellow10-14 daysISP 3
19926Cream10-14 daysISP 4
19926Green brown10-14 daysISP 5
19926Green brown10-14 daysISP 6
19926Green brown10-14 daysISP 7
610312 days

multicellular morphology

@refforms multicellular complexmedium name
19926noISP 2
19926noISP 3
19926noISP 4
19926noISP 5
19926noISP 6
19926noISP 7

pigmentation

@refproduction
29393no
29345yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15894GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
15894GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19926ISP 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
19926ISP 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:
19926ISP 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
19926ISP 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
19926ISP 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
19926ISP 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
15894N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
15894COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
15894ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15894positivegrowth28mesophilic
29345positivegrowth20-37
29393positivegrowth27-37mesophilic
61031positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29393aerobe
29345aerobe
61031microaerophile

spore formation

@refspore formationconfidence
29345yes
29393yes
69481yes100
69480yes100

observation

  • @ref: 29345
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1992617234glucose+
1992622599arabinose+/-
1992617992sucrose+
1992618222xylose-
1992617268myo-inositol+
1992629864mannitol+
1992628757fructose+
1992626546rhamnose-
1992616634raffinose-
1992662968cellulose+/-
29345620642,3-butanediol+carbon source
2934530089acetate+carbon source
2934517128adipate+carbon source
2934515963ribitol+carbon source
2934516449alanine+carbon source
2934522599arabinose+carbon source
2934529016arginine+carbon source
2934517057cellobiose+carbon source
2934516947citrate+carbon source
2934528260galactose+carbon source
293455291gelatin+carbon source
2934524265gluconate+carbon source
2934517234glucose+carbon source
2934524996lactate+carbon source
2934517716lactose+carbon source
2934517306maltose+carbon source
2934529864mannitol+carbon source
2934518257ornithine+carbon source
2934526271proline+carbon source
2934517822serine+carbon source
2934517992sucrose+carbon source
2934527082trehalose+carbon source
2939316449alanine+carbon source
2939329016arginine+carbon source
2939317057cellobiose+carbon source
2939324996lactate+carbon source
2939317716lactose+carbon source
2939318257ornithine+carbon source
2939326271proline+carbon source
2939326546rhamnose+carbon source
2939317822serine+carbon source
2939330911sorbitol+carbon source
293454853esculin+hydrolysis
293934853esculin+hydrolysis

enzymes

@refvalueactivityec
29393urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19926+++-++--+++---++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
15894household wasteStuttgartGermanyDEUEurope
61031Household wasteStuttgartGermanyDEUEurope1995

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Engineered#Waste#Domestic waste

taxonmaps

  • @ref: 69479
  • File name: preview.99_6085.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_2754;97_3390;98_4514;99_6085&stattab=map
  • Last taxonomy: Nocardiopsis potens
  • 16S sequence: FM253114
  • Sequence Identity:
  • Total samples: 23
  • soil counts: 14
  • aquatic counts: 3
  • animal counts: 6

Safety information

risk assessment

  • @ref: 15894
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15894
  • description: Nocardiopsis sp. IMMIB L-21 partial 16S rRNA gene, type strain IMMIB L-21
  • accession: FM253114
  • length: 1498
  • database: ena
  • NCBI tax ID: 570268

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis potens DSM 45234GCA_000341105contigncbi570268
66792Nocardiopsis potens DSM 45234570268.3wgspatric570268
66792Nocardiopsis potens DSM 452342554235031draftimg570268

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.776no
anaerobicno99.188yes
halophileno56.769no
spore-formingyes92.865yes
glucose-utilyes87.57yes
thermophileno96.059yes
flagellatedno97.842yes
aerobicyes91.311no
motileno92.506yes
glucose-fermentno90.877no

External links

@ref: 15894

culture collection no.: DSM 45234, CCUG 56587, IMMIB L-21

straininfo link

  • @ref: 80472
  • straininfo: 403394

literature

  • topic: Phylogeny
  • Pubmed-ID: 19625427
  • title: Nocardiopsis potens sp. nov., isolated from household waste.
  • authors: Yassin AF, Sproer C, Hupfer H, Siering C, Klenk HP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.011288-0
  • year: 2009
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Environmental Microbiology, *Housing, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Refuse Disposal
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15894Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45234)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45234
19926Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45234.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
29345Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2575728776041
29393Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2580028776041
61031Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56587)https://www.ccug.se/strain?id=56587
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)
68382Automatically annotated from API zym
69479João 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
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
80472Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403394.1StrainInfo: A central database for resolving microbial strain identifiers