Strain identifier

BacDive ID: 10726

Type strain: Yes

Species: Nocardia pseudobrasiliensis

Strain history: CIP <- 1995, R. Ruimy, CNRS, Villefranche/Mer, France <- R.J. Wallace, Texas, USA

NCBI tax ID(s): 1210086 (strain), 45979 (species)

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General

@ref: 11647

BacDive-ID: 10726

DSM-Number: 44290

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, spore-forming, mesophilic, Gram-positive

description: Nocardia pseudobrasiliensis DSM 44290 is a microaerophile, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from leg abscess of a patient suffering from ulcerative colitis.

NCBI tax id

NCBI tax idMatching level
45979species
1210086strain

strain history

@refhistory
11647<- CCUG <- CIP
67770CIP 104600 <-- R. Ruimy <-- R. J. Wallace N224 <-- D. Delgado.
121983CIP <- 1995, R. Ruimy, CNRS, Villefranche/Mer, France <- R.J. Wallace, Texas, USA

doi: 10.13145/bacdive10726.20230509.8.1

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 pseudobrasiliensis
  • full scientific name: Nocardia pseudobrasiliensis Ruimy et al. 1996

@ref: 11647

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia pseudobrasiliensis

full scientific name: Nocardia pseudobrasiliensis Ruimy et al. 1996

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shape
69480positive100
121983positiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19646Yellow orange10-14 daysISP 2
19646Yellow orange10-14 daysISP 3
19646Yellow orange10-14 daysISP 4
19646Yellow orange10-14 daysISP 5
19646Yellow orange10-14 daysISP 6
19646Yellow orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19646yesAerial MyceliumWhiteISP 2
19646yesAerial MyceliumWhiteISP 3
19646yesAerial MyceliumWhiteISP 4
19646yesAerial MyceliumWhiteISP 5
19646noISP 6
19646yesAerial MyceliumWhiteISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
11647https://www.dsmz.de/microorganisms/photos/DSM_44290-1.jpg© Leibniz-Institut DSMZ
11647https://www.dsmz.de/microorganisms/photos/DSM_44290.jpg© Leibniz-Institut DSMZMedium 535 37°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11647TRYPTICASE 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
19646ISP 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
19646ISP 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:
19646ISP 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
19646ISP 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
19646ISP 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
19646ISP 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
41381MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121983CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
19646positiveoptimum37mesophilic
11647positivegrowth37mesophilic
41381positivegrowth30mesophilic
52726positivegrowth37mesophilic
67770positivegrowth28mesophilic
121983positivegrowth30-37mesophilic
121983nogrowth10psychrophilic
121983nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
52726microaerophile
121983obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 97

halophily

@refsaltgrowthtested relationconcentration
19646NaClpositivegrowth0 %
121983NaClpositivegrowth0-4 %
121983NaClnogrowth6 %
121983NaClnogrowth8 %
121983NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
1219834853esculin-hydrolysis
121983606565hippurate+hydrolysis
12198317632nitrate-reduction
12198316301nitrite-reduction
121983132112sodium thiosulfate-builds gas from
12198317632nitrate-respiration
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12198335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-
12198315688acetoin-

enzymes

@refvalueactivityec
68379catalase+1.11.1.6
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379alpha-glucosidase+3.2.1.20
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
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
121983oxidase-
121983beta-galactosidase+3.2.1.23
121983alcohol dehydrogenase-1.1.1.1
121983gelatinase+
121983amylase-
121983DNase-
121983caseinase+3.4.21.50
121983catalase+1.11.1.6
121983tween esterase-
121983lecithinase-
121983lipase-
121983lysine decarboxylase-4.1.1.18
121983ornithine decarboxylase-4.1.1.17
121983urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382trypsin+3.4.21.4
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-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    52726C16:036.116
    52726C18:02.718
    52726C16:1 ω7c/C15:0 ISO 2OH27.215.85
    52726C18:1 ω9c8.217.769
    52726C18:2 ω6,9c/C18:0 ANTE4.417.724
    52726TBSA 10Me18:018.818.392
    52726Unidentified2.618.56
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
19646-+++-++++++--------
52726--++--+-++----------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19646+++++++++++-+-++++-
52726+++-+--+-++---++----
121983+++-++-+-++-+-++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19646------+--++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121983+-++--------------++-----------++--------------+-+----+----+---------------+---++-------+++--++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11647leg abscess of a patient suffering from ulcerative colitis
52726Human leg abscessTexasUSAUSANorth America
67770Leg abscess
121983Human, Leg abscessTexasUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Infection#Patient
#Host Body-Site#Other#Abscess
#Host Body-Site#Limb#Leg

taxonmaps

  • @ref: 69479
  • File name: preview.99_4707.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_448;98_3531;99_4707&stattab=map
  • Last taxonomy: Nocardia pseudobrasiliensis
  • 16S sequence: X84857
  • Sequence Identity:
  • Total samples: 57
  • soil counts: 52
  • animal counts: 4
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116472Risk group (German classification)
196462Risk group (German classification)
1219832Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia pseudobrasiliensis clone A20 16S ribosomal RNA gene, partial sequenceAY262309500ena45979
20218Nocardia pseudobrasiliensis strain ATCC 51512 16S ribosomal RNA gene, partial sequenceDQ6599141350ena45979
20218Nocardia pseudobrasiliensis strain ATCC 51512 16S ribosomal RNA gene, partial sequenceGQ3761821439ena45979
20218N.pseudobrasiliensis 16S rRNA gene (ATCC 51512)X848571407ena45979
20218Nocardia pseudobrasiliensis strain DSM 44290 16S ribosomal RNA gene, complete sequenceAF4300421492ena45979
20218Nocardia pseudobrasiliensis strain DSM 44290 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536471323ena45979
20218Nocardia pseudobrasiliensis strain DSM 44290 16S ribosomal RNA gene, partial sequenceAY756558606ena45979
20218Nocardia pseudobrasiliensis strain DSM 44290 16S ribosomal RNA gene, partial sequenceJN041521462ena45979

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia pseudobrasiliensis NBRC 1082241210086.4wgspatric1210086
66792Nocardia pseudobrasiliensis strain DSM 4429045979.5wgspatric45979
66792Nocardia pseudobrasiliensis NBRC 1082242731957744draftimg1210086
66792Nocardia pseudobrasiliensis DSM 442902770939519draftimg45979
67770Nocardia pseudobrasiliensis NBRC 108224GCA_001613105contigncbi1210086
67770Nocardia pseudobrasiliensis DSM 44290GCA_003350585scaffoldncbi45979

GC content

@refGC-contentmethod
1164767.1
6777067.1capillary zone electrophoresis (CZE)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes97no
motileno93.756no
gram-positiveyes87.162no
anaerobicno99.119yes
aerobicyes87.861yes
halophileno91.405no
spore-formingyes85.065no
glucose-utilyes88.707no
flagellatedno98.17no
thermophileno98.726no
glucose-fermentno91.115yes

External links

@ref: 11647

culture collection no.: DSM 44290, ATCC 51512, CCUG 35436, CIP 104600, JCM 9894, CGMCC 4.1880, IFM 0624, NBRC 108224

straininfo link

  • @ref: 79994
  • straininfo: 43028

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8573505Nocardia pseudobrasiliensis sp. nov., a new species of Nocardia which groups bacterial strains previously identified as Nocardia brasiliensis and associated with invasive diseases.Ruimy R, Riegel P, Carlotti A, Boiron P, Bernardin G, Monteil H, Wallace RJ Jr, Christen RInt J Syst Bacteriol10.1099/00207713-46-1-2591996DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Nocardia/chemistry/*classification/genetics/metabolism, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, PhylogenyGenetics
Metabolism9402986Nocardicyclins A and B: new anthracycline antibiotics produced by Nocardia pseudobrasiliensis.Tanaka Y, Grafe U, Yazawa K, Mikami Y, Ritzau MJ Antibiot (Tokyo)10.7164/antibiotics.50.8221997*Anthracyclines, Antibiotics, Antineoplastic/*chemistry/metabolism/*pharmacology, Fermentation, Magnetic Resonance Spectroscopy, Microbial Sensitivity Tests, Molecular Structure, Nocardia/chemistry/*metabolism
Phylogeny26873179Nocardia rayongensis sp. nov., isolated from Thai peat swamp forest soil.Tanasupawat S, Phongsopitanun W, Suwanborirux K, Ohkuma M, Kudo TInt J Syst Evol Microbiol10.1099/ijsem.0.0009712016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Forests, Nocardia/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsTranscriptome
Phylogeny32815801Nocardia macrotermitis sp. nov. and Nocardia aurantia sp. nov., isolated from the gut of the fungus-growing termite Macrotermes natalensis.Benndorf R, Schwitalla JW, Martin K, de Beer ZW, Vollmers J, Kaster AK, Poulsen M, Beemelmanns CInt J Syst Evol Microbiol10.1099/ijsem.0.0043982020Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gastrointestinal Microbiome, Isoptera/*microbiology, Nocardia/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, South Africa, Vitamin K 2/analogs & derivatives/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11647Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44290)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44290
19646Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44290.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
41381Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16526
52726Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35436)https://www.ccug.se/strain?id=35436
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
79994Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43028.1StrainInfo: A central database for resolving microbial strain identifiers
121983Curators of the CIPCollection of Institut Pasteur (CIP 104600)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104600