Strain identifier

BacDive ID: 10784

Type strain: Yes

Species: Nocardia yamanashiensis

Strain history: CIP <- 2004, DSMZ <- Y. Mikami, Chiba, Japan: strain IFM 0265

NCBI tax ID(s): 1210099 (strain), 209247 (species)

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General

@ref: 11865

BacDive-ID: 10784

DSM-Number: 44669

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

description: Nocardia yamanashiensis DSM 44669 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from human.

NCBI tax id

NCBI tax idMatching level
209247species
1210099strain

strain history

@refhistory
11865<- Y. Mikami; IFM 0265
67770Y. Mikami IFM 0265 <-- Natl. Defense Med. Coll., Japan.
124008CIP <- 2004, DSMZ <- Y. Mikami, Chiba, Japan: strain IFM 0265

doi: 10.13145/bacdive10784.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Nocardia
  • species: Nocardia yamanashiensis
  • full scientific name: Nocardia yamanashiensis Kageyama et al. 2004

@ref: 11865

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia yamanashiensis

full scientific name: Nocardia yamanashiensis Kageyama et al. 2004 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29989positiverod-shapedno
69480no93.904
69480positive100
124008positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20090Pastel yellow (1034)10-14 daysISP 2
20090Beige (1001)10-14 daysISP 3
20090Beige (1001)10-14 daysISP 4
20090Beige (1001)10-14 daysISP 5
20090Beige (1001)10-14 daysISP 6
20090Pastel yellow (1034)10-14 daysISP 7
124008

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20090yesAerial MyceliumWhiteISP 2
20090yesAerial MyceliumWhiteISP 3
20090noISP 4
20090noISP 5
20090noISP 6
20090noISP 7

multimedia

  • @ref: 11865
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44669.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11865TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
11865GYM 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
20090ISP 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
20090ISP 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:
20090ISP 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
20090ISP 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
20090ISP 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
20090ISP 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
40000MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
124008CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57
124008CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
11865positivegrowth28mesophilic
20090positiveoptimum28mesophilic
29989positiveoptimum37mesophilic
40000positivegrowth30mesophilic
67770positivegrowth28mesophilic
124008positivegrowth30mesophilic
124008nogrowth10psychrophilic
124008nogrowth25mesophilic
124008nogrowth37mesophilic
124008nogrowth41thermophilic
124008nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 124008
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
124008NaClpositivegrowth0-4 %
124008NaClnogrowth6 %
124008NaClnogrowth8 %
124008NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4, ω-cycl)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2009017234glucose+
2009022599arabinose-
2009017992sucrose-
2009018222xylose-
2009017268myo-inositol+
2009029864mannitol-
2009028757fructose-
2009026546rhamnose-
2009016634raffinose-
2009062968cellulose-
2998916947citrate+carbon source
2998924265gluconate+carbon source
2998917234glucose+carbon source
2998937684mannose+carbon source
12400816947citrate-carbon source
1240084853esculin+hydrolysis
124008606565hippurate-hydrolysis
12400817632nitrate+reduction
12400816301nitrite-reduction
12400817632nitrate-respiration
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose+fermentation

antibiotic resistance

  • @ref: 124008
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 124008
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12400815688acetoin-
12400817234glucose-

enzymes

@refvalueactivityec
29989urease+3.5.1.5
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
124008oxidase-
124008beta-galactosidase+3.2.1.23
124008alcohol dehydrogenase-1.1.1.1
124008gelatinase-
124008amylase-
124008DNase-
124008caseinase-3.4.21.50
124008catalase+1.11.1.6
124008tween esterase-
124008gamma-glutamyltransferase+2.3.2.2
124008lecithinase-
124008lipase-
124008lysine decarboxylase-4.1.1.18
124008ornithine decarboxylase-4.1.1.17
124008phenylalanine ammonia-lyase-4.3.1.24
124008tryptophan deaminase-
124008urease+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-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
20090--+--+-++-+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20090++++++-+-++---++---
124008++++++-+-++-+-+++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
124008+-----------+-----++-----------++--------------+-++--+-----+------------++++-+-++-----+-+-+++++-+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11865humanJapanJPNAsia
67770Skin abscessJapanJPNAsia
124008HumanJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_866.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_448;98_685;99_866&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: GQ853072
  • Sequence Identity:
  • Total samples: 287
  • soil counts: 266
  • aquatic counts: 9
  • animal counts: 7
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118652Risk group (German classification)
1240082Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia yamanashiensis strain DSM 44669 isolate VNS34 16S ribosomal RNA gene, partial sequenceAY903616606ena209247
20218Nocardia yamanashiensis strain DSM 44669 16S ribosomal RNA gene, partial sequenceDQ6599201434ena209247
20218Nocardia yamanashiensis strain W8187 16S ribosomal RNA gene, partial sequenceGQ8530721439ena209247
11865Nocardia yamanashiensi gene for 16S rRNA, partial sequence, strain:IFM 0265AB0925611499ena209247

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia yamanashiensis NBRC 1001301210099.4wgspatric1210099
66792Nocardia yamanashiensis NBRC 1001302731957750draftimg1210099
67770Nocardia yamanashiensis NBRC 100130GCA_001613325contigncbi1210099

GC content

@refGC-contentmethod
1186569.2
6777069.2high performance liquid chromatography (HPLC)
6777068.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.062yes
gram-positiveyes90.569no
anaerobicno99.65no
aerobicyes92.566no
halophileno95.828no
spore-formingyes88.473no
thermophileno99.448no
glucose-utilyes89.809no
flagellatedno98.009yes
glucose-fermentno90.606no

External links

@ref: 11865

culture collection no.: DSM 44669, JCM 11893, NBRC 100130, IFM 0265, CIP 108422

straininfo link

  • @ref: 80049
  • straininfo: 131430

literature

  • topic: Phylogeny
  • Pubmed-ID: 15023976
  • title: Nocardia inohanensis sp. nov., Nocardia yamanashiensis sp. nov. and Nocardia niigatensis sp. nov., isolated from clinical specimens.
  • authors: Kageyama A, Yazawa K, Nishimura K, Mikami Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02794-0
  • year: 2004
  • mesh: Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Humans, Microscopy, Electron, Scanning, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification/ultrastructure, Nocardia Infections/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
11865Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44669)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44669
20090Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44669.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
29989Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126356
40000Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6043
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/
68379Automatically annotated from API Coryne
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
80049Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131430.1StrainInfo: A central database for resolving microbial strain identifiers
124008Curators of the CIPCollection of Institut Pasteur (CIP 108422)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108422