Strain identifier

BacDive ID: 10742

Type strain: Yes

Species: Nocardia nova

Strain Designation: 23095, 2338, R443(1), R443

Strain history: CIP <- 1996, IFO <- 1993, JCM <- M. Tsukamura: strain 23095 <- R.E. Gordon: strain R443 <- I.B. Christison <- N.F. Conant: strain 2338

NCBI tax ID(s): 1210081 (strain), 37330 (species)

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General

@ref: 11807

BacDive-ID: 10742

DSM-Number: 44481

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, human pathogen

description: Nocardia nova 23095 is an aerobe, mesophilic human pathogen that builds an aerial mycelium.

NCBI tax id

NCBI tax idMatching level
37330species
1210081strain

strain history

@refhistory
11807<- JCM <- M. Tsukamura; 23095 <- R. E. Gordon; R443(1) <- I. B. Christison <- N. F. Conant; 2338
67770M. Tsukamura 23095 <-- R. E. Gordon R443 (1) <-- I. B. Christison <-- N. F. Conant 2338.
121361CIP <- 1996, IFO <- 1993, JCM <- M. Tsukamura: strain 23095 <- R.E. Gordon: strain R443 <- I.B. Christison <- N.F. Conant: strain 2338

doi: 10.13145/bacdive10742.20230509.8.1

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 nova
  • full scientific name: Nocardia nova Tsukamura 1983

@ref: 11807

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia nova

full scientific name: Nocardia nova Tsukamura 1983 emend. Nouioui et al. 2018

strain designation: 23095, 2338, R443(1), R443

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.009
69480100positive
121361positiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20062Pastel yellow (1034)10-14 daysISP 2
20062Pastel yellow (1034)10-14 daysISP 3
20062Pastel yellow (1034)10-14 daysISP 4
20062Pastel yellow (1034)10-14 daysISP 5
569962 days

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20062yesAerial MyceliumWhiteISP 2
20062noISP 3
20062noISP 4
20062noISP 5
20062noISP 6
20062noISP 7

multimedia

  • @ref: 11807
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44481.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11807TRYPTICASE 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
11807GYM 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
20062ISP 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
20062ISP 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:
20062ISP 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
20062ISP 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
35233MEDIUM 9 - Brain heart infusion BHIyesDistilled water make up to (1000.000 ml);Brain heart infusion (37.000 g)
121361CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116
121361CIP Medium 9yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=9
121361CIP Medium 129yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=129
121361CIP Medium 194yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=194

culture temp

@refgrowthtypetemperaturerange
11807positivegrowth28mesophilic
35233positivegrowth30mesophilic
56996positivegrowth37mesophilic
67770positivegrowth28mesophilic
121361positivegrowth30-37mesophilic
121361nogrowth10psychrophilic
121361nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
56996aerobe
121361obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.565

halophily

@refsaltgrowthtested relationconcentration
20062NaClpositivemaximum2.5 %
121361NaClpositivegrowth0-4 %
121361NaClnogrowth6 %
121361NaClnogrowth8 %
121361NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1213614853esculin-hydrolysis
121361606565hippurate+hydrolysis
12136117632nitrate+reduction
12136116301nitrite-reduction
12136117632nitrate-respiration

metabolite production

@refmetaboliteproductionChebi-ID
67770nocardimicin Gyes
67770nocardimicin Hyes
67770nocardimicin Iyes
68368acetoinno15688
68368indoleno35581
68368hydrogen sulfideno16136
121361indoleno35581

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-
12136115688acetoin-

enzymes

@refvalueactivityec
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
121361oxidase-
121361beta-galactosidase+3.2.1.23
121361alcohol dehydrogenase-1.1.1.1
121361gelatinase-
121361amylase-
121361DNase-
121361caseinase-3.4.21.50
121361catalase+1.11.1.6
121361tween esterase-
121361lecithinase-
121361lysine decarboxylase-4.1.1.18
121361ornithine decarboxylase-4.1.1.17
121361urease+3.5.1.5
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382alpha-chymotrypsin-3.4.21.1
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 zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20062--+-++--------++---
121361+++-++++-++-+-++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20062-++++------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121361+------------------------------------------------+-------------------------+--+++-------+-+-----+-+

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_3476.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_448;98_513;99_3476&stattab=map
  • Last taxonomy: Nocardia nova
  • 16S sequence: X80593
  • Sequence Identity:
  • Total samples: 47
  • soil counts: 25
  • aquatic counts: 11
  • animal counts: 6
  • plant counts: 5

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
11807yesyes2Risk group (German classification)
200622German classification
1213612Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia nova strain JCM 6044 16S ribosomal RNA gene, complete sequenceAF4300281492ena37330
20218Nocardia nova strain JCM 6044 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536455322ena37330
20218Nocardia nova strain JCM 6044 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536456322ena37330
20218Nocardia nova strain JCM 6044 note copy 3 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536457328ena37330
20218Nocardia nova strain ATCC 33726T 16S ribosomal RNA gene, partial sequenceAY1912501383ena37330
20218Nocardia nova clone A9 16S ribosomal RNA gene, partial sequenceAY262320500ena37330
20218Nocardia nova strain ATCC 33726 16S ribosomal RNA gene, partial sequenceDQ6599111401ena37330
20218Nocardia nova strain ATCC 33726 16S ribosomal RNA gene, partial sequenceGQ3761901439ena37330
20218Nocardia nova strain ATCC 33726 clone 1 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236409626ena37330
20218Nocardia nova strain ATCC 33726 clone 2 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236410626ena37330
20218Nocardia nova strain ATCC 33726 clone 3 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236411626ena37330
20218Nocardia nova strain ATCC 33726 clone 4 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236412626ena37330
20218Nocardia nova strain ATCC 33726 clone 5 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236413632ena37330
20218Nocardia nova strain ATCC 33726 clone 6 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236414626ena37330
20218Nocardia nova strain DSM 44481 16S ribosomal RNA gene, partial sequenceJN041650462ena37330
11807Nocardia nova 16S rRNA gene, strain ATCC 33726TX805931395ena37330
11807N.nova gene for 16S ribosomal RNAZ369301472ena37330

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia nova NBRC 155561210081.4wgspatric1210081
66792Nocardia nova NBRC 155562731957739draftimg1210081
67770Nocardia nova NBRC 15556GCA_001613005contigncbi1210081

GC content

@refGC-contentmethod
1180767.3high performance liquid chromatography (HPLC)
6777067.9genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes83no
motileno93.995no
gram-positiveyes84.283no
anaerobicno98.305yes
aerobicyes85.384no
halophileno92.527no
spore-formingyes78.775no
glucose-utilyes87.28no
flagellatedno98.354no
thermophileno99.155yes
glucose-fermentno92.112no

External links

@ref: 11807

culture collection no.: DSM 44481, ATCC 33726, CCRC 13746, CIP 104777, IFM 0290, IFO 15556, JCM 6044, NBRC 15556, CCUG 45939, BCRC 13746, CECT 3056, CGMCC 4.1705, CGMCC 4.1879, IMSNU 21197, IMSNU 21201, KCTC 9959, VKM Ac-1971

straininfo link

  • @ref: 80010
  • straininfo: 40652

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny6763136Numerical analysis of the taxonomy of Nocardiae and Rhodococci.Tsukamura MMicrobiol Immunol10.1111/j.1348-0421.1982.tb00260.x1982Actinomycetales/*classification/growth & development, Drug Resistance, Microbial, Humans, Lung Diseases/etiology, Nocardia/*classification/drug effects/growth & development, Nocardia Infections/complications/microbiology, Nocardia asteroides/growth & developmentPathogenicity
Enzymology16320761Nocardimicins G, H and I, siderophores with muscarinic M3 receptor binding inhibitory activity from Nocardia nova JCM 6044.Ikeda Y, Furumai T, Igarashi YJ Antibiot (Tokyo)10.1038/ja.2005.772005Hydroxamic Acids/isolation & purification/pharmacology, Molecular Structure, Muscarinic Antagonists/chemistry/isolation & purification/pharmacokinetics/pharmacology, Nocardia/*chemistry, Oxazoles/isolation & purification/pharmacology, Receptor, Muscarinic M3/*antagonists & inhibitors/metabolism, Siderophores/chemistry/*isolation & purification/pharmacologyPhylogeny
Phylogeny19684327Nocardia callitridis sp. nov., an endophytic actinobacterium isolated from a surface-sterilized root of an Australian native pine tree.Kaewkla O, Franco CMMInt J Syst Evol Microbiol10.1099/ijs.0.016337-02009Australia, Base Sequence, Fatty Acids/analysis, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification/physiology, Pinus/*microbiology, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, SterilizationGenetics
Phylogeny20817835Nocardia endophytica sp. nov., an endophytic actinomycete isolated from the oil-seed plant Jatropha curcas L.Xing K, Qin S, Fei SM, Lin Q, Bian GK, Miao Q, Wang Y, Cao CL, Tang SK, Jiang JH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.027391-02010DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Jatropha/*microbiology/physiology, Molecular Sequence Data, Nocardia/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, SymbiosisGenetics
Phylogeny24475340Terrestrial actinomycetes from diverse locations of Uttarakhnad, India: Isolation and screening for their antibacterial activity.Kumar V, Bisht GS, Gusain OIran J Microbiol2013
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
Phylogeny29845487Nocardia zhihengii sp. nov., an actinobacterium isolated from rhizosphere soil of Psammosilene tunicoides.Huang MJ, Xiao M, Rao MPN, Cheng T, Yang YY, Alkhalifah DHM, Hozzein WN, Huang HQ, Li WJAntonie Van Leeuwenhoek10.1007/s10482-018-1107-82018Base Composition/genetics, Caryophyllaceae/*microbiology, Nocardia/chemistry/*genetics/*isolation & purification, Phosphatidylglycerols/analysis, Phylogeny, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
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
Phylogeny35412966Nocardia albiluteola sp. nov., a novel lignin-degrading actinobacterium isolated from rhizosphere soil of pumpkin.Shan Q, Han C, Zhao J, Yu B, Jiang M, Liu T, Wang X, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0053052022*Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, *Cucurbita, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lignin, *Nocardia, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11807Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44481)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44481
20062Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44481.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
35233Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16723
56996Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45939)https://www.ccug.se/strain?id=45939
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
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)
80010Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40652.1StrainInfo: A central database for resolving microbial strain identifiers
121361Curators of the CIPCollection of Institut Pasteur (CIP 104777)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104777