Strain identifier

BacDive ID: 10790

Type strain: Yes

Species: Nocardia testacea

Strain history: CIP <- 2004, JCM <- 2003, Y. Mikami, IFM, Japan

NCBI tax ID(s): 1206739 (strain), 248551 (species)

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General

@ref: 12072

BacDive-ID: 10790

DSM-Number: 44765

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, human pathogen

description: Nocardia testacea DSM 44765 is an obligate aerobe, spore-forming, mesophilic human pathogen that builds an aerial mycelium and was isolated from human.

NCBI tax id

NCBI tax idMatching level
1206739strain
248551species

strain history

@refhistory
12072<- Y. Mikami, IFM
67770Y. Mikami IFM 0937.
123482CIP <- 2004, JCM <- 2003, Y. Mikami, IFM, Japan

doi: 10.13145/bacdive10790.20230509.8.1

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 testacea
  • full scientific name: Nocardia testacea corrig. Kageyama et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Nocardia testaceus

@ref: 12072

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia testacea

full scientific name: Nocardia testacea Kageyama et al. 2004

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.043
69480100positive
123482nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20111Pastel orange (2003)10-14 daysISP 2
20111Pastel orange (2003)10-14 daysISP 3
20111Pastel orange (2003)10-14 daysISP 4
20111Pastel orange (2003)10-14 daysISP 5
20111Pastel orange (2003)10-14 daysISP 6
20111Pastel orange (2003)10-14 daysISP 7
123482

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20111yesAerial MyceliumBeige redISP 2
20111noISP 3
20111noISP 4
20111noISP 5
20111noISP 6
20111noISP 7

multimedia

  • @ref: 12072
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44765.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12072TRYPTICASE 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
12072GYM 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
20111ISP 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
20111ISP 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:
20111ISP 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
20111ISP 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
20111ISP 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
20111ISP 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
34959MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123482CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116
123482CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
12072positivegrowth28mesophilic
20111positiveoptimum28mesophilic
34959positivegrowth25mesophilic
67770positivegrowth28mesophilic
123482positivegrowth25-41
123482nogrowth10psychrophilic
123482nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123482
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480no98.209

halophily

@refsaltgrowthtested relationconcentration
123482NaClpositivegrowth0-4 %
123482NaClnogrowth6 %
123482NaClnogrowth8 %
123482NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2011117234glucose+
2011122599arabinose-
2011117992sucrose-
2011118222xylose-
2011117268myo-inositol-
2011129864mannitol-
2011128757fructose-
2011126546rhamnose-
2011116634raffinose-
2011162968cellulose-
12348216947citrate-carbon source
1234824853esculin-hydrolysis
123482606565hippurate-hydrolysis
12348217632nitrate+reduction
12348216301nitrite-reduction
12348217632nitrate-respiration
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose+fermentation

antibiotic resistance

  • @ref: 123482
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123482
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12348215688acetoin-
12348217234glucose-

enzymes

@refvalueactivityec
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
123482oxidase-
123482beta-galactosidase-3.2.1.23
123482alcohol dehydrogenase-1.1.1.1
123482gelatinase-
123482amylase-
123482DNase-
123482caseinase-3.4.21.50
123482catalase+1.11.1.6
123482tween esterase-
123482gamma-glutamyltransferase-2.3.2.2
123482lecithinase-
123482lipase-
123482lysine decarboxylase-4.1.1.18
123482ornithine decarboxylase-4.1.1.17
123482phenylalanine ammonia-lyase-4.3.1.24
123482tryptophan deaminase-
123482urease-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
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
20111-++----+--+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20111+++-++-+-++----+---
123482+++-++---++----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12072humanJapanJPNAsia
67770Sputum of a patient with nontuberculous mycobacterial infectionJapanJPNAsia
123482Human, SputumJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_3551.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_658;98_2723;99_3551&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: JF797319
  • Sequence Identity:
  • Total samples: 11377
  • soil counts: 8278
  • aquatic counts: 469
  • animal counts: 943
  • plant counts: 1687

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12072yes, in single cases1Risk group (German classification)
201112German classification
1234822Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia testacea strain DSM 44765 isolate SVN09 16S ribosomal RNA gene, partial sequenceAY903612606ena248551
20218Nocardia testacea strain DSM 44765 16S ribosomal RNA gene, partial sequenceJF7973191412ena248551
20218Nocardia testacea gene for 16S rRNA, partial sequenceAB1217691333ena248551
20218Nocardia testacea gene for 16S rRNA, partial sequenceAB1924151487ena248551

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia testacea NBRC 1003651206739.4wgspatric1206739
66792Nocardia testacea NBRC 1003652551306161draftimg1206739
67770Nocardia testacea NBRC 100365GCA_000308775contigncbi1206739

GC content

@refGC-contentmethod
6777068.5genome sequence analysis
6777068.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.008no
gram-positiveyes89.891no
anaerobicno99.212no
aerobicyes90.322no
halophileno91.962no
spore-formingyes74.792no
thermophileno98.927no
glucose-utilyes87.361yes
flagellatedno98.423no
glucose-fermentno91.482no

External links

@ref: 12072

culture collection no.: DSM 44765, IFM 0937, JCM 12235, CIP 108506, NBRC 100365

straininfo link

  • @ref: 80055
  • straininfo: 132792

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15107537Nocardia testaceus sp. nov. and Nocardia senatus sp. nov., isolated from patients in Japan.Kageyama A, Yazawa K, Nishimura K, Mikami YMicrobiol Immunol10.1111/j.1348-0421.2004.tb03523.x2004DNA, Ribosomal/analysis, Humans, Japan, Molecular Sequence Data, Nocardia/*classification/genetics/*isolation & purification/metabolism, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sputum/microbiologyPathogenicity
Phylogeny21596508Nocardia rhamnosiphila sp. nov., isolated from soil.Everest GJ, Cook AE, le Roes-Hill M, Meyers PRSyst Appl Microbiol10.1016/j.syapm.2011.03.0062011Bacterial Typing Techniques, Base Sequence, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Genotype, Microbial Sensitivity Tests, Molecular Sequence Data, Nocardia/chemistry/*classification/genetics/*isolation & purification/physiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12072Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44765)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44765
20111Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44765.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
34959Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6136
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
80055Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132792.1StrainInfo: A central database for resolving microbial strain identifiers
123482Curators of the CIPCollection of Institut Pasteur (CIP 108506)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108506