Strain identifier

BacDive ID: 10654

Type strain: Yes

Species: Nocardia brevicatena

Strain Designation: 0029

Strain history: CIP <- 1995, IFO <- KCC: strain 0029 <- H.A. Chevalier: strain IMRU 1086W

NCBI tax ID(s): 1206725 (strain), 37327 (species)

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General

@ref: 10695

BacDive-ID: 10654

DSM-Number: 43024

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

description: Nocardia brevicatena 0029 is an obligate aerobe, spore-forming human pathogen that was isolated from sputum of patient with tuberculosis.

NCBI tax id

NCBI tax idMatching level
37327species
1206725strain

strain history

@refhistory
10695<- KCC <- H. Lechevalier
67770KCC A-0029 <-- IMRU 1086.
117004CIP <- 1995, IFO <- KCC: strain 0029 <- H.A. Chevalier: strain IMRU 1086W

doi: 10.13145/bacdive10654.20240916.9.1

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 brevicatena
  • full scientific name: Nocardia brevicatena (Lechevalier et al. 1961) Goodfellow and Pirouz 1982

  • synonyms

    • @ref: 20215
    • synonym: Micropolyspora brevicatena

@ref: 10695

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia brevicatena

full scientific name: Nocardia brevicatena (Lechevalier et al. 1961) Goodfellow and Pirouz 1982 emend. Nouioui et al. 2018

strain designation: 0029

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
117004positiverod-shapedno
69480no91.5
69480positive93.074

colony morphology

@refcolony colorincubation periodmedium used
19537Orange10-14 daysISP 2
19537Orange10-14 daysISP 3
19537Orange10-14 daysISP 4
19537Orange10-14 daysISP 5
19537Bright orange10-14 daysISP 6
1953710-14 daysISP 7
117004

multicellular morphology

@refforms multicellular complexmedium name
19537noISP 2
19537noISP 3
19537noISP 4
19537noISP 5
19537noISP 6
19537noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10695CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
10695BHI-GLUCOSE MEDIUM (DSMZ Medium 82)yeshttps://mediadive.dsmz.de/medium/82Name: BHI-GLUCOSE MEDIUM (DSMZ Medium 82) Composition: Brain heart infusion 18.5 g/l Agar 12.0 g/l Glucose 5.0 g/l Distilled water
19537ISP 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
19537ISP 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:
19537ISP 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
19537ISP 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
19537ISP 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
19537ISP 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
37964MEDIUM 128 - for Nocardia brevicatena, Nocardia flavorosea subsp. fusca and Streptomyces ambofaciensyesDistilled water make up to (1000.000 ml);Maltose (10.000 g);Agar (20.000g);Yeast extract (1.000 g);Beef extract (1.000 g);Casamino acids (2.000 g)
117004CIP Medium 129yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=129

culture temp

@refgrowthtypetemperature
19537positiveoptimum28
10695positivegrowth37
37964positivegrowth30
67770positivegrowth37
117004positivegrowth25-41
117004nogrowth10
117004nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 117004
  • oxygen tolerance: obligate aerobe

spore formation

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

halophily

@refsaltgrowthtested relationconcentration
19537NaClpositivemaximum2.5 %
117004NaClpositivegrowth0-4 %
117004NaClnogrowth6 %
117004NaClnogrowth8 %
117004NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1953717234glucose+
1953722599arabinose+
1953717992sucrose+
1953718222xylose+
1953717268myo-inositol+
1953729864mannitol+
1953728757fructose+
1953726546rhamnose+
1953716634raffinose+
1953762968cellulose+
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
1170044853esculin+hydrolysis
117004606565hippurate-hydrolysis
11700417632nitrate-reduction
11700416301nitrite-reduction
11700417632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11700435581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
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
117004oxidase-
117004beta-galactosidase+3.2.1.23
117004alcohol dehydrogenase-1.1.1.1
117004gelatinase-
117004catalase+1.11.1.6
117004gamma-glutamyltransferase-2.3.2.2
117004lysine decarboxylase-4.1.1.18
117004ornithine decarboxylase-4.1.1.17
117004urease+3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
10695-+/-++------------+---
117004-+++-+----++----+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19537----+-+--+-

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
10695-----+++-----++-++/---

Isolation, sampling and environmental information

isolation

@refsample type
10695sputum of patient with tuberculosis
67770Sputum
117004Human, Sputum

isolation source categories

Cat1Cat2Cat3
#Infection#Disease#Tuberculosis
#Infection#Patient
#Host Body-Site#Oral cavity and airways#Lung
#Host Body Product#Fluids#Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_5286.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_3135;98_3937;99_5286&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: X80600
  • Sequence Identity:
  • Total samples: 1410
  • soil counts: 1068
  • aquatic counts: 52
  • animal counts: 144
  • plant counts: 146

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
10695yes, in single cases1Risk group (German classification)
195371Hazard group
1170042Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia brevicatena strain DSM 43024 16S ribosomal RNA gene, partial sequenceAY756545606nuccore1206725
20218Nocardia brevicatena strain ATCC 15333 16S ribosomal RNA gene, partial sequenceDQ6599031436nuccore1206725
20218Nocardia brevicatena strain W9965 16S ribosomal RNA gene, partial sequenceGQ8530811441nuccore37327
20218Nocardia brevicatena strain ATCC 15333 clone 1 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236345635nuccore1206725
20218Nocardia brevicatena strain ATCC 15333 clone 2 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236346635nuccore1206725
20218Nocardia brevicatena strain ATCC 15333 clone 3 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236347635nuccore1206725
20218Nocardia brevicatena NBRC 12119 strain ATCC 15333 16S ribosomal RNA gene, partial sequenceJN041588462nuccore1206725
20218Nocardia brevicatena 16S rRNA gene, strain ATCC 15333TX806001395nuccore1206725
20218Nocardia brevicatena NBRC 12119 strain DSM 43024 16S ribosomal RNA gene, complete sequenceAF4300401494nuccore1206725
20218Nocardia brevicatena strain DSM 43024 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536407329nuccore1206725
20218N.brevicatena gene for 16S ribosomal RNAZ369281474nuccore1206725

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia brevicatena NBRC 121191206725.5wgspatric1206725
66792Nocardia brevicatena NBRC 121192551306159draftimg1206725
67770Nocardia brevicatena NBRC 12119GCA_000308495contigncbi1206725

GC content

@refGC-contentmethod
6777067.5
6777067genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes93.074no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.947yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes56.611no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.624yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.4yes
69480flagellatedmotile2+Ability to perform flagellated movementno91.5no

External links

@ref: 10695

culture collection no.: DSM 43024, ATCC 15333, IFO 12119, IMRU 1086, KCC A-0029, NBRC 12119, RIA 709, CCUG 46115, JCM 3029, BCRC 13389, CGMCC 4.1163, CIP 104508, IFM 0283, IMET 9542, IMSNU 20103, IMSNU 21207, KCCM 12521, KCTC 9370, NRRL B-2896, VKM Ac-936, IMRU 1086W

straininfo link

  • @ref: 79924
  • straininfo: 36338

literature

  • topic: Phylogeny
  • Pubmed-ID: 26914251
  • title: Nocardia donostiensis sp. nov., isolated from human respiratory specimens.
  • authors: Ercibengoa M, Bell M, Marimon JM, Humrighouse B, Klenk HP, Potter G, Perez-Trallero E
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-016-0667-8
  • year: 2016
  • mesh: Adolescent, Aged, Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Humans, Male, Nocardia/*classification/genetics/*isolation & purification, Nocardia Infections/*microbiology, Phenotype, Phylogeny, Pneumonia, Bacterial/*microbiology, RNA, Ribosomal, 16S/genetics, Respiratory System/*microbiology
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10695Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43024)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43024
19537Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43024.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
37964Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16425
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
68369Automatically annotated from API 20NE
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
79924Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36338.1StrainInfo: A central database for resolving microbial strain identifiers
117004Curators of the CIPCollection of Institut Pasteur (CIP 104508)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104508