Strain identifier

BacDive ID: 11175

Type strain: Yes

Species: Nocardiopsis listeri

Strain Designation: 203

Strain history: KCC S-0782 <-- IFO 13360 <-- SAJ <-- ISP 5297 <-- NCTC 434 <-- D. Erikson.

NCBI tax ID(s): 1348637 (strain), 53440 (species)

« back to strain detail view
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: 9441

BacDive-ID: 11175

DSM-Number: 40297

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

description: Nocardiopsis listeri 203 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from human clinical isolate.

NCBI tax id

NCBI tax idMatching level
53440species
1348637strain

strain history

@refhistory
9441<- E.B. Shirling, ISP (Streptomyces listeri) <- NCTC <- D. Erikson, Lister Inst., 203
67770KCC S-0782 <-- IFO 13360 <-- SAJ <-- ISP 5297 <-- NCTC 434 <-- D. Erikson.

doi: 10.13145/bacdive11175.20230509.8.1

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 listeri
  • full scientific name: Nocardiopsis listeri Grund and Kroppenstedt 1990

@ref: 9441

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis listeri

full scientific name: Nocardiopsis listeri Grund and Kroppenstedt 1990 emend. Nouioui et al. 2018

strain designation: 203

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
19434Ivory10-14 daysISP 2
19434Ivory10-14 daysISP 3
19434Ivory10-14 daysISP 4
19434Ivory10-14 daysISP 5
19434Ivory10-14 daysISP 6
19434Ivory10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19434noISP 2
19434noISP 3
19434noISP 4
19434noISP 5
19434noISP 6
19434noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9441GYM 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
19434ISP 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
19434ISP 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:
19434ISP 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
19434ISP 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
19434ISP 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
19434ISP 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

culture temp

@refgrowthtypetemperaturerange
9441positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 100

halophily

  • @ref: 19434
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-10(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
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
19434+++-++-++++++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19434+--------++

Isolation, sampling and environmental information

isolation

@refsample type
9441human clinical isolate
67770Human

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Infection#Patient
#Infection#Medical environment#Clinic
#Infection#Patient#Specimen

taxonmaps

  • @ref: 69479
  • File name: preview.99_7519.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_5510;99_7519&stattab=map
  • Last taxonomy: Nocardiopsis listeri subclade
  • 16S sequence: X97887
  • Sequence Identity:
  • Total samples: 469
  • soil counts: 55
  • aquatic counts: 41
  • animal counts: 365
  • plant counts: 8

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
94411Risk group (German classification)
194341Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: N.listeri 16S rRNA gene
  • accession: X97887
  • length: 1463
  • database: ena
  • NCBI tax ID: 53440

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis listeri NBRC 133601348637.3wgspatric1348637
66792Nocardiopsis listeri NBRC 133602731957603draftimg1348637
67770Nocardiopsis listeri NBRC 13360GCA_001570765contigncbi1348637

GC content

  • @ref: 67770
  • GC-content: 68.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes82no
motileno91.583no
gram-positiveyes91.673no
anaerobicno99.257no
halophileyes75.437no
spore-formingyes92.651no
thermophileno97.631no
glucose-utilyes88.996no
aerobicyes94.057no
flagellatedno97.598no
glucose-fermentno90.356no

External links

@ref: 9441

culture collection no.: DSM 40297, ATCC 27442, CBS 661.72, CGMCC AS 4.1445, IFO 13360, ISP 5297, KCC S-0782, NBRC 13360, NCTC 434, PCM 2491, RIA 1321, JCM 4782, BCRC 15134, CGMCC 4.1445, CGMCC 4.2110, NRRL B-2782, VKM Ac-1881

straininfo link

  • @ref: 80424
  • straininfo: 13392

literature

  • topic: Genetics
  • Pubmed-ID: 9526113
  • title: Teichoic acids of the cell wall of Nocardiopsis listeri, Nocardiopsis lucentensis, and Nocardiopsis tregalosei.
  • authors: Streshinskaya GM, Tul'skaya EM, Shashkov AS, Evtushenko LI, Taran VV, Naumova IB
  • journal: Biochemistry (Mosc)
  • year: 1998
  • mesh: Actinomycetales/*chemistry, Carbohydrate Sequence, Cell Wall/chemistry, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Species Specificity, Teichoic Acids/*chemistry
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9441Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40297)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40297
19434Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40297.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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/
68368Automatically annotated from API 20E
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)
80424Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13392.1StrainInfo: A central database for resolving microbial strain identifiers