Strain identifier

BacDive ID: 10777

Type strain: Yes

Species: Nocardia shimofusensis

Strain history: CIP <- 2004, DSMZ <- IFM

NCBI tax ID(s): 1210087 (strain), 228596 (species)

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General

@ref: 12051

BacDive-ID: 10777

DSM-Number: 44733

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

description: Nocardia shimofusensis DSM 44733 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
228596species
1210087strain

strain history

@refhistory
12051<- Y. Mikami, IFM
67770Y. Mikami IFM 10311.
122589CIP <- 2004, DSMZ <- IFM

doi: 10.13145/bacdive10777.20230509.8.1

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 shimofusensis
  • full scientific name: Nocardia shimofusensis Kageyama et al. 2004

@ref: 12051

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia shimofusensis

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

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31216positive1.35 µm0.6 µmrod-shapedno
69480no95.946
69480positive100
122589positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19700Pastel yellow10-14 daysISP 2
1970010-14 daysISP 3
1970010-14 daysISP 4
1970010-14 daysISP 5
19700Pastel yellow10-14 daysISP 6
1970010-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19700noISP 2
19700noISP 3
19700noISP 4
19700noISP 5
19700noISP 6
19700noISP 7

pigmentation

  • @ref: 31216
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12051GYM 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
19700ISP 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
19700ISP 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:
19700ISP 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
19700ISP 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
19700ISP 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
19700ISP 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
40034MEDIUM 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)
122589CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
12051positivegrowth28mesophilic
19700positiveoptimum28mesophilic
40034positivegrowth30mesophilic
67770positivegrowth28mesophilic
122589positivegrowth10-41
122589nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31216aerobe
122589obligate aerobe

spore formation

@refspore formationconfidence
69481yes92
69480no99.943

halophily

@refsaltgrowthtested relationconcentration
122589NaClpositivegrowth0-6 %
122589NaClnogrowth8 %
122589NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1970017234glucose-
1970022599arabinose-
1970017992sucrose-
1970018222xylose-
1970017268myo-inositol-
1970029864mannitol-
1970028757fructose-
1970026546rhamnose-
1970016634raffinose-
1970062968cellulose-
12258916947citrate-carbon source
1225894853esculin-hydrolysis
122589606565hippurate+hydrolysis
12258917632nitrate+reduction
12258916301nitrite-reduction
12258917632nitrate-respiration
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

antibiotic resistance

  • @ref: 122589
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122589
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12258915688acetoin-
12258917234glucose-

enzymes

@refvalueactivityec
31216urease+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
122589oxidase-
122589beta-galactosidase-3.2.1.23
122589alcohol dehydrogenase-1.1.1.1
122589gelatinase-
122589amylase-
122589DNase-
122589caseinase-3.4.21.50
122589catalase+1.11.1.6
122589tween esterase-
122589gamma-glutamyltransferase-2.3.2.2
122589lecithinase-
122589lipase-
122589lysine decarboxylase-4.1.1.18
122589ornithine decarboxylase-4.1.1.17
122589phenylalanine ammonia-lyase-4.3.1.24
122589tryptophan deaminase-
122589urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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 coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
19700-++--+-----

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19700+++++----++---++---
122589+++-+----++---++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122589+--++--+-++--------------------------------------------------+----------++++---+++--------------+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
12051soilJapanJPNAsia
67770SoilJapanJPNAsiaChoshi, Chiba Pref.
122589Environment, SoilJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4240.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_280;98_506;99_4240&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: JF797315
  • Sequence Identity:
  • Total samples: 12
  • soil counts: 4
  • aquatic counts: 1
  • animal counts: 5
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120511Risk group (German classification)
197001Risk group (German classification)
1225892Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia shimofusensis strain DSM 44733 isolate VNS39 16S ribosomal RNA gene, partial sequenceAY903621606ena228596
20218Nocardia shimofusensis 16S ribosomal RNA gene, partial sequenceGQ3761871441ena228596
20218Nocardia shimofusensis strain DSM 44733 16S ribosomal RNA gene, partial sequenceJF7973151414ena228596
12051Nocardia shimofusensis gene for 16S rRNA, partial sequence, strain:YZ-96AB1087751508ena228596

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia shimofusensis NBRC 1001341210087.4wgspatric1210087
66792Nocardia shimofusensis NBRC 1001342731957745draftimg1210087
67770Nocardia shimofusensis NBRC 100134GCA_001613125contigncbi1210087

GC content

@refGC-contentmethod
1205168-69
3121668.5
6777069.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes92no
motileno94.945yes
gram-positiveyes88.293no
anaerobicno99.107yes
aerobicyes88.564yes
halophileno92.531no
spore-formingyes78.335no
glucose-utilyes82.195yes
flagellatedno98.48yes
thermophileno98.614yes
glucose-fermentno92.793no

External links

@ref: 12051

culture collection no.: DSM 44733, CIP 108598, IFM 10311, JCM 12122, NBRC 100134

straininfo link

  • @ref: 80043
  • straininfo: 134456

literature

  • topic: Phylogeny
  • Pubmed-ID: 15545412
  • title: Nocardia shimofusensis sp. nov., isolated from soil, and Nocardia higoensis sp. nov., isolated from a patient with lung nocardiosis in Japan.
  • authors: Kageyama A, Yazawa K, Mukai A, Kinoshita M, Takata N, Nishimura K, Kroppenstedt RM, Mikami Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63061-0
  • year: 2004
  • mesh: Aged, Antimetabolites/pharmacology, Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Female, Fluorouracil/pharmacology, Genes, rRNA, Humans, Japan, Lung/*microbiology, Molecular Sequence Data, Nocardia/chemistry/*classification/drug effects/genetics/*isolation & purification/metabolism, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12051Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44733)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44733
19700Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44733.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
31216Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127542
40034Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6245
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
80043Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134456.1StrainInfo: A central database for resolving microbial strain identifiers
122589Curators of the CIPCollection of Institut Pasteur (CIP 108598)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108598