Strain identifier

BacDive ID: 11180

Type strain: Yes

Species: Nocardiopsis alba

Strain Designation: A 92

Strain history: DSM 43377 <-- M. Goodfellow A92 (Nocardiopsis dassonvillei) <-- W. A. Causey CDC W2536.

NCBI tax ID(s): 53437 (species)

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General

@ref: 10994

BacDive-ID: 11180

DSM-Number: 43377

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

description: Nocardiopsis alba A 92 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from drainage from hip.

NCBI tax id

  • NCBI tax id: 53437
  • Matching level: species

strain history

@refhistory
10994<- M. Goodfellow, A 92 (Actinomadura dassonvillei) <- W.A. Causey, CDC, W2536 (Nocardiopsis dasonvillei)
67770DSM 43377 <-- M. Goodfellow A92 (Nocardiopsis dassonvillei) <-- W. A. Causey CDC W2536.

doi: 10.13145/bacdive11180.20230509.8.1

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 alba
  • full scientific name: Nocardiopsis alba corrig. Grund and Kroppenstedt 1990

  • synonyms

    • @ref: 20215
    • synonym: Nocardiopsis albus

@ref: 10994

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Not assigned to order

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis alba

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

strain designation: A 92

type strain: yes

Morphology

cell morphology

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

multimedia

  • @ref: 10994
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43377.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10994GPHF-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
10994GYM 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

culture temp

@refgrowthtypetemperaturerange
18489positiveoptimum28mesophilic
10994positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes91
69480yes100

halophily

  • @ref: 18489
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-10(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1848917234glucose+
1848922599arabinose-
1848917992sucrose+
1848918222xylose-
1848917268myo-inositol-
1848929864mannitol+
1848928757fructose-
1848926546rhamnose-
1848916634raffinose-
1848962968cellulose-
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
18489+++-+++--++---++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18489+++++-+--++

Isolation, sampling and environmental information

isolation

@refsample type
10994drainage from hip
67770Drainage from hip

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Fluids#Aspirate
#Host#Human
#Host Body-Site#Limb#Leg

taxonmaps

  • @ref: 69479
  • File name: preview.99_1537.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_1213;99_1537&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: X97883
  • Sequence Identity:
  • Total samples: 350
  • soil counts: 41
  • aquatic counts: 19
  • animal counts: 284
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184891German classification
109941Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: N.alba 16S rRNA gene, strain DSM 43377T
  • accession: X97883
  • length: 1461
  • database: ena
  • NCBI tax ID: 1245473

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis alba DSM 433771245473.3wgspatric1245473
66792Nocardiopsis alba DSM 433772551306665draftimg1245473
67770Nocardiopsis alba DSM 43377GCA_000341225contigncbi1245473

GC content

  • @ref: 67770
  • GC-content: 69.8
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes91no
motileno92.467no
gram-positiveyes93.016no
anaerobicno99.325no
aerobicyes93.048no
halophileyes70.177no
spore-formingyes92.772no
glucose-utilyes87.033yes
flagellatedno97.42no
thermophileno96.636yes
glucose-fermentno91.256no

External links

@ref: 10994

culture collection no.: DSM 43377, JCM 9419, CDC W2536, BCRC 16256, IFM 10232, IFO 15097, IMSNU 22172, KCTC 9616, NBRC 15097, VKM Ac-1883, VTT E-99143

straininfo link

  • @ref: 80429
  • straininfo: 265470

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9336896Description of Nocardiopsis synnemataformans sp. nov., elevation of Nocardiopsis alba subsp. prasina to Nocardiopsis prasina comb. nov., and designation of Nocardiopsis antarctica and Nocardiopsis alborubida as later subjective synonyms of Nocardiopsis dassonvillei.Yassin AF, Rainey FA, Burghardt J, Gierth D, Ungerechts J, Lux I, Seifert P, Bal C, Schaal KPInt J Syst Bacteriol10.1099/00207713-47-4-9831997Base Composition, Culture Media, Conditioned/metabolism, DNA, Bacterial/*analysis, Humans, Microscopy, Electron, Molecular Sequence Data, Propionibacteriaceae/chemistry/*classification/genetics/growth & development/metabolism/ultrastructure, RNA, Ribosomal, 16S/*analysisCultivation
Phylogeny25380720Nocardiopsis algeriensis sp. nov., an alkalitolerant actinomycete isolated from Saharan soil.Bouras N, Meklat A, Zitouni A, Mathieu F, Schumann P, Sproer C, Sabaou N, Klenk HPAntonie Van Leeuwenhoek10.1007/s10482-014-0329-72014Actinobacteria/*classification/genetics/*isolation & purification/physiology, Africa, Northern, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Spores, Bacterial/cytology, Temperature, Vitamin K 2/analysisGenetics
33820119Novel cell-wall teichoic acid from Nocardiopsis albus subsp. albus as a species-specific marker.Tul'skaya EM, Shashkov AS, Evtushenko LI, Taran VV, Naumova IBMicrobiology (Reading)10.1099/13500872-141-8-18511995
Metabolism34758070Two strains of airborne Nocardiopsis alba producing different volatile organic compounds (VOCs) as biofungicide for Ganoderma boninense.Widada J, Damayanti E, Alhakim MR, Yuwono T, Mustofa MFEMS Microbiol Lett10.1093/femsle/fnab1382021Air Microbiology, Antifungal Agents/pharmacology, Fungicides, Industrial/metabolism/pharmacology, *Ganoderma/drug effects, Nocardiopsis/chemistry/metabolism, Species Specificity, *Volatile Organic Compounds/metabolism/pharmacologyPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10994Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43377)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43377
18489Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43377.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)
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
80429Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265470.1StrainInfo: A central database for resolving microbial strain identifiers