Strain identifier

BacDive ID: 10794

Type strain: Yes

Species: Nocardia thailandica

Strain history: CIP <- 2005, JCM <- 2004, IFM

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 12093

BacDive-ID: 10794

DSM-Number: 44808

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

description: Nocardia thailandica DSM 44808 is an obligate aerobe, spore-forming, mesophilic human pathogen that was isolated from human.

NCBI tax id

NCBI tax idMatching level
1206740strain
257275species

strain history

@refhistory
12093<- Y. Mikami, IFM
67770Y. Mikami IFM 10145.
123497CIP <- 2005, JCM <- 2004, IFM

doi: 10.13145/bacdive10794.20230509.8.1

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 thailandica
  • full scientific name: Nocardia thailandica Kageyama et al. 2005

@ref: 12093

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia thailandica

full scientific name: Nocardia thailandica Kageyama et al. 2005

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.388
69480100positive
123497nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20123Rose (3017)10-14 daysISP 2
2012310-14 daysISP 3
2012310-14 daysISP 4
20123Saffron yellow (1017)10-14 daysISP 5
20123Saffron yellow (1017)10-14 daysISP 6
20123Saffron yellow (1017)10-14 daysISP 7
123497

multicellular morphology

@refforms multicellular complexmedium name
20123noISP 2
20123noISP 3
20123noISP 4
20123noISP 5
20123noISP 6
20123noISP 7

multimedia

  • @ref: 12093
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44808.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12093TRYPTICASE 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
20123ISP 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
20123ISP 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:
20123ISP 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
20123ISP 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
20123ISP 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
20123ISP 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
38301MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
123497CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
12093positivegrowth28mesophilic
20123positiveoptimum28mesophilic
38301positivegrowth30mesophilic
67770positivegrowth28mesophilic
123497positivegrowth25-41
123497nogrowth10psychrophilic
123497nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123497
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes95
69480no99.355

halophily

@refsaltgrowthtested relationconcentration
123497NaClpositivegrowth0-4 %
123497NaClnogrowth6 %
123497NaClnogrowth8 %
123497NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2012317234glucose+
2012322599arabinose-
2012317992sucrose-
2012318222xylose+
2012317268myo-inositol-
2012329864mannitol-
2012328757fructose+
2012326546rhamnose-
2012316634raffinose-
2012362968cellulose-
12349716947citrate-carbon source
1234974853esculin+hydrolysis
123497606565hippurate-hydrolysis
12349717632nitrate+reduction
12349716301nitrite-reduction
12349717632nitrate-respiration
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

metabolite production

  • @ref: 123497
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12349715688acetoin-
12349717234glucose-

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
123497oxidase-
123497beta-galactosidase-3.2.1.23
123497alcohol dehydrogenase-1.1.1.1
123497gelatinase-
123497amylase-
123497DNase-
123497caseinase-3.4.21.50
123497catalase+1.11.1.6
123497tween esterase-
123497gamma-glutamyltransferase+2.3.2.2
123497lecithinase-
123497lipase-
123497lysine decarboxylase-4.1.1.18
123497ornithine decarboxylase-4.1.1.17
123497phenylalanine ammonia-lyase-4.3.1.24
123497tryptophan deaminase-
123497urease+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
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
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
20123--+--+-----

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20123++++++---++---++---
123497+++-++-+-++-+-++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123497++-+---------------------------+---------------------------+---------------+--+---------+--+---++--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12093humanThailandTHAAsia
67770Pus of a patientThailandTHAAsia
123497Human, PusThailandTHAAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12093yes, in single cases1Risk group (German classification)
1234972Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia thailandica strain DSM 44808 16S ribosomal RNA gene, partial sequenceJF7973201412ena257275
20218Nocardia thailandica strain DSM 44808 16S ribosomal RNA gene, partial sequenceJN041449462ena257275
20218Nocardia thailandica gene for 16S rRNA, partial sequenceAB1268741440ena257275
20218Nocardia thailandica 16S ribosomal RNA gene, partial sequenceGQ3761861439ena257275
20218Nocardia testacea strain W9870 16S ribosomal RNA gene, partial sequenceGQ8530701439ena248551

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia thailandica NBRC 1004281206740.4wgspatric1206740
66792Nocardia thailandica NBRC 1004282551306162draftimg1206740
67770Nocardia thailandica NBRC 100428GCA_000308795contigncbi1206740

GC content

@refGC-contentmethod
6777071.7genome sequence analysis
6777072high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes95no
motileno92.704no
gram-positiveyes89.599no
anaerobicno99.628no
halophileno93.375no
spore-formingyes72.216no
thermophileno99.392no
glucose-utilyes88.654yes
flagellatedno97.859no
aerobicyes93.22no
glucose-fermentno93.116no

External links

@ref: 12093

culture collection no.: DSM 44808, IFM 10145, JCM 12356, CIP 108722, NBRC 100428

straininfo link

  • @ref: 80059
  • straininfo: 138030

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12093Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44808)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44808
20123Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44808.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
38301Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6382
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
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
80059Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138030.1StrainInfo: A central database for resolving microbial strain identifiers
123497Curators of the CIPCollection of Institut Pasteur (CIP 108722)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108722