Strain identifier

BacDive ID: 10655

Type strain: Yes

Species: Nocardia carnea

Strain Designation: 30

Strain history: CIP <- 1995, IFO <- 1984, ATCC <- NCTC, Actinomyces carneus <- V. Puntoni: strain 30

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General

@ref: 10805

BacDive-ID: 10655

DSM-Number: 43397

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

description: Nocardia carnea 30 is an aerobe, spore-forming, mesophilic human pathogen of the family Nocardiaceae.

NCBI tax id

NCBI tax idMatching level
37328species
1206726strain

strain history

@refhistory
10805<- R.E. Gordon, IMRU <- V. Putoni
67770CIP 104509 <-- IFO 14403 <-- ATCC 6847 <-- NCTC 3527 <-- V. Puntoni; 30.
117186CIP <- 1995, IFO <- 1984, ATCC <- NCTC, Actinomyces carneus <- V. Puntoni: strain 30

doi: 10.13145/bacdive10655.20230509.8.1

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 carnea
  • full scientific name: Nocardia carnea (Rossi Doria 1891) Castellani and Chalmers 1913 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Streptothrix carnea

@ref: 10805

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia carnea

full scientific name: Nocardia carnea (Rossi Doria 1891) Castellani and Chalmers 1913 emend. Nouioui et al. 2018

strain designation: 30

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.908
69480100positive
117186positiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10805GYM 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
41222MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
117186CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18491positiveoptimum30mesophilic
10805positivegrowth30mesophilic
41222positivegrowth30mesophilic
58021positivegrowth30-37mesophilic
67770positivegrowth28mesophilic
117186positivegrowth30-37mesophilic
117186nogrowth10psychrophilic
117186nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58021aerobe
117186obligate aerobe

spore formation

@refspore formationconfidence
69481yes94
69480no98.477

halophily

@refsaltgrowthtested relationconcentration
18491NaClpositivemaximum7.5 %
117186NaClpositivegrowth0-6 %
117186NaClnogrowth8 %
117186NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1849117234glucose+
1849122599arabinose-
1849117992sucrose-
1849118222xylose-
1849117268myo-inositol-
1849129864mannitol+
1849128757fructose-
1849126546rhamnose-
1849116634raffinose-
1849162968cellulose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
117186606565hippurate+hydrolysis
11718617632nitrate+reduction
11718616301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11718635581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-
11718615688acetoin-

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
117186oxidase-
117186beta-galactosidase+3.2.1.23
117186alcohol dehydrogenase-1.1.1.1
117186gelatinase-
117186amylase-
117186DNase-
117186caseinase-3.4.21.50
117186catalase+1.11.1.6
117186tween esterase-
117186lecithinase-
117186lysine decarboxylase-4.1.1.18
117186ornithine decarboxylase-4.1.1.17
117186urease-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
68382trypsin-3.4.21.4
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117186-+++-+----++----+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18491------+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
117186------------------+------------------------------+------------++--+------------++-------+-+-----+--

Isolation, sampling and environmental information

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: X80607
  • 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
10805yes, in single cases1Risk group (German classification)
184911
1171862Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia carnea NBRC 14403 16S ribosomal RNA gene, partial sequenceGQ3761651439ena1206726
20218Nocardia carnea strain ATCC 6847 clone 1 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236349625ena1206726
20218Nocardia carnea strain ATCC 6847 clone 2 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236350625ena1206726
20218Nocardia carnea strain ATCC 6847 clone 3 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236351625ena1206726
20218Nocardia carnea strain ATCC 6847 clone 4 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236352625ena1206726
20218Nocardia carnea strain ATCC 6847 clone 5 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236353625ena1206726
20218Nocardia carnea strain ATCC 6847 clone 6 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236354625ena1206726
20218Nocardia carnea strain ATCC 6847 16S ribosomal RNA gene, partial sequenceJF7973071412ena1206726
20218Nocardia carnea 16S rRNA gene, strain ATCC 6847TX806021395ena1206726
20218Nocardia carnea strain CGMCC 4.1167 clone 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceDQ518337331ena1206726
20218Nocardia carnea strain CGMCC 4.1167 clone 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceDQ518338325ena1206726
20218Nocardia carnea strain DSM 43397 16S ribosomal RNA gene, complete sequenceAF4300351492ena1206726
20218Nocardia carnea strain DSM 43397 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536408321ena1206726
20218Nocardia carnea strain DSM 43397 16S ribosomal RNA gene, partial sequenceAY756546606ena1206726
20218Nocardia carnea 16S rRNA gene, strain DSM43397TX806071463ena1206726
20218N.carnea gene for 16S ribosomal RNAZ369291472ena1206726
20218Nocardia carnea strain NRRL B-1336 16S ribosomal RNA gene, partial sequenceJN041599462ena37328

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia carnea NBRC 144031206726.4wgspatric1206726
66792Nocardia carnea NBRC 144032551306165draftimg1206726
67770Nocardia carnea NBRC 14403GCA_000308515contigncbi1206726

GC content

@refGC-contentmethod
6777068fluorimetric
6777067.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes94no
motileno92.764no
gram-positiveyes86.11no
anaerobicno99.43yes
aerobicyes90.324yes
halophileno82.076no
spore-formingyes76.49no
glucose-utilyes91.076yes
flagellatedno98.463no
thermophileno98.974no
glucose-fermentno92.911no

External links

@ref: 10805

culture collection no.: CCUG 48177, CIP 104509, IFO 14403, JCM 3375, NRRL B-1336, DSM 43397, ATCC 6847, IMRU 3419, NCTC 3527, DSM 43580, JCM 30727, BCRC 13693, CCM 2756, CGMCC 4.1167, CGMCC 4.1733, IFM 0237, IMET 7504, IMSNU 21185, KCTC 9957, NBRC 14403, VKM Ac-814

straininfo link

  • @ref: 79925
  • straininfo: 92194

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734044Nocardia flavorosea sp. nov.Chun J, Seong CN, Bae KS, Lee KJ, Kang SO, Goodfellow M, Hah YCInt J Syst Bacteriol10.1099/00207713-48-3-9011998Base Sequence, DNA, Ribosomal/chemistry, Molecular Sequence Data, Nocardia/*classification, RNA, Ribosomal, 16S/geneticsGenetics
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
10805Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43397)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43397
18491Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43397.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
41222Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16426
58021Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48177)https://www.ccug.se/strain?id=48177
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)
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
79925Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92194.1StrainInfo: A central database for resolving microbial strain identifiers
117186Curators of the CIPCollection of Institut Pasteur (CIP 104509)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104509