Strain identifier

BacDive ID: 10669

Type strain: Yes

Species: Nocardia farcinica

Strain Designation: GA 919 (N 164), M 258

Strain history: CIP <- 1996, IFO <- 1993, NCIMB <- NCTC <- 1976, ATCC, Nocardia asteroides <- 1957, R.E. Gordon

NCBI tax ID(s): 1210076 (strain), 37329 (species)

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General

@ref: 11231

BacDive-ID: 10669

DSM-Number: 43665

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

description: Nocardia farcinica GA 919 is an obligate aerobe, spore-forming, mesophilic human pathogen that was isolated from madura foot.

NCBI tax id

NCBI tax idMatching level
37329species
1210076strain

strain history

@refhistory
11231<- M. Ridell, GA 919 (N 164) <- M. Goodfellow, M 258 <- M.P. Lechevalier <- ATCC (Nocardia asteroides) <- R.E. Gordon
67770KCC A-0088 <-- IFM 0028 <-- N. M. McClung <-- ATCC 3318 <-- R. E. Gordon <-- S. A. Waksman 3318.
119283CIP <- 1996, IFO <- 1993, NCIMB <- NCTC <- 1976, ATCC, Nocardia asteroides <- 1957, R.E. Gordon

doi: 10.13145/bacdive10669.20230509.8.1

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 farcinica
  • full scientific name: Nocardia farcinica Trevisan 1889 (Approved Lists 1980)

@ref: 11231

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia farcinica

full scientific name: Nocardia farcinica Trevisan 1889 emend. Nouioui et al. 2018

strain designation: GA 919 (N 164), M 258

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.95
69480100positive
119283positiverod-shaped

multimedia

  • @ref: 11231
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43665.jpg
  • caption: Medium 553 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11231GYM 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
11231GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
119283CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119283CIP Medium 146yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=146

culture temp

@refgrowthtypetemperaturerange
18497positiveoptimum30mesophilic
11231positivegrowth37mesophilic
67770positivegrowth37mesophilic
119283positivegrowth30-45
119283nogrowth10psychrophilic

culture pH

@refabilitytypepH
18497positivemaximum8
18497positiveminimum5

Physiology and metabolism

oxygen tolerance

  • @ref: 119283
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes98
69480no98.588

halophily

@refsaltgrowthtested relationconcentration
18497NaClpositivemaximum2.5 %
119283NaClpositivegrowth0-6 %
119283NaClnogrowth8 %
119283NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1849717234glucose+
1849722599arabinose-
1849717992sucrose+
1849718222xylose-
1849717268myo-inositol-
1849729864mannitol-
1849728757fructose-
1849726546rhamnose+
1849716634raffinose-
1849762968cellulose+/-
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
119283606565hippurate-hydrolysis
11928317632nitrate+reduction
11928316301nitrite-reduction
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-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
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11928335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-
11928315688acetoin-

enzymes

@refvalueactivityec
68379catalase+1.11.1.6
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
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
119283oxidase+
119283beta-galactosidase+3.2.1.23
119283alcohol dehydrogenase-1.1.1.1
119283gelatinase-
119283DNase-
119283caseinase-3.4.21.50
119283catalase+1.11.1.6
119283tween esterase-
119283lecithinase-
119283lysine decarboxylase-4.1.1.18
119283ornithine decarboxylase-4.1.1.17
119283urease+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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
11231+--+----+-----------+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119283-+++-++++-++-+-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18497------+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119283-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119283++-+-------------------+-------------------+-----+-----------+----+--------+--+++--+++--+-------+-+

Isolation, sampling and environmental information

isolation

@refsample type
11231madura foot
119283Madura foot

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Limb#Foot
#Infection#Disease
#Infection#Patient
#Host#Fungi

taxonmaps

  • @ref: 69479
  • File name: preview.99_1854.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_280;98_506;99_1854&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: X80610
  • Sequence Identity:
  • Total samples: 1055
  • soil counts: 406
  • aquatic counts: 189
  • animal counts: 365
  • plant counts: 95

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
11231yesyes2Risk group (German classification)
184972German classification
1192832Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia farcinica clone A8 16S ribosomal RNA gene, partial sequenceAY262321500ena37329
20218Nocardia farcinica strain ATCC 3318 16S ribosomal RNA gene, partial sequenceDQ6599061389ena37329
20218Nocardia farcinica culture collection CDC:W6977 16S ribosomal RNA gene, partial sequenceGQ2174991441ena37329
20218Nocardia farcinica strain W6977 16S ribosomal RNA gene, partial sequenceGQ8530651441ena37329
20218Nocardia farcinica strain ATCC 3318 clone 1 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236387640ena37329
20218Nocardia farcinica strain ATCC 3318 clone 2 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236388640ena37329
20218Nocardia farcinica strain ATCC 3318 clone 3 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236389644ena37329
20218Nocardia farcinica strain ATCC 3318 clone 4 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236390644ena37329
20218Nocardia farcinica 16S rRNA gene, strain ATCC 3318X805951394ena37329
20218N.farcinica gene for 16S ribosomal RNAZ369361474ena37329
20218Nocardia farcinica strain CGMCC 4.1166 16S-23S ribosomal RNA intergenic spacer, complete sequenceDQ518339341ena37329
20218Nocardia farcinica strain DSM 43665 16S ribosomal RNA gene, partial sequenceAY756551606ena37329
20218Nocardia farcinica strain DSM 43665 16S ribosomal RNA gene, complete sequenceAF4300331494ena37329
20218Nocardia farcinica strain DSM 43665 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536445338ena37329
20218Nocardia farcinica strain DSM 43665 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536446334ena37329
20218Nocardia farcinica 16S rRNA gene, strain DSM43665TX806101465ena37329
20218Nocardia farcinica strain NRRL B-2089 16S ribosomal RNA gene, partial sequenceJN041682462ena37329

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia farcinica NCTC11134GCA_001182745completencbi37329
66792Nocardia farcinica NBRC 155321210076.5wgspatric1210076
66792Nocardia farcinica strain DSM 4325737329.5wgspatric37329
66792Nocardia farcinica strain NCTC1113437329.11plasmidpatric37329
66792Nocardia farcinica strain NCTC1113437329.10plasmidpatric37329
66792Nocardia farcinica strain NCTC1113437329.9plasmidpatric37329
66792Nocardia farcinica strain NCTC1113437329.8plasmidpatric37329
66792Nocardia farcinica NBRC 155322731957735draftimg1210076
66792Nocardia farcinica NCTC111342663763270completeimg37329
66792Nocardia farcinica DSM 432572681813555draftimg37329
67770Nocardia farcinica NBRC 15532GCA_001612925contigncbi1210076
67770Nocardia farcinica DSM 43257GCA_900156775contigncbi37329

GC content

@refGC-contentmethod
6777070.7genome sequence analysis
6777070.2high performance liquid chromatography (HPLC)
6777068fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes98no
motileno93.217no
flagellatedno97.943no
gram-positiveyes89.736no
anaerobicno99.296no
aerobicyes87.802no
halophileno86.606no
spore-formingyes84.306no
glucose-utilyes88.445yes
thermophileno98.11yes
glucose-fermentno91.862no

External links

@ref: 11231

culture collection no.: DSM 43665, ATCC 3318, DSM 43257, DSM 43578, IMRU 3318, NCIB 12058, NCTC 11134, JCM 3088, BCRC 13380, BCRC 13722, CBS 318.60, CCUG 10109, CCUG 27778, CCUG 48656, CECT 3053, CECT 4069, CGMCC 4.1166, CGMCC 4.1829, CIP 104775, IFM 0028, IFM 0284, IFO 15532, IMET 7377, IMSNU 21224, KCTC 9958, NBRC 15532, NCIMB 12058, NRRL B-2089, PCM 2173

straininfo link

  • @ref: 79939
  • straininfo: 70749

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24198056Nocardia kroppenstedtii sp. nov., an actinomycete isolated from a lung transplant patient with a pulmonary infection.Jones AL, Fisher AJ, Mahida R, Gould K, Perry JD, Hannan MM, Judge EP, Brown R, Boagey K, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.048330-02013Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Humans, Lung Diseases/*microbiology, Lung Transplantation, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPathogenicity
Metabolism28065456Characterization and functional expression of a rubber degradation gene of a Nocardia degrader from a rubber-processing factory.Linh DV, Huong NL, Tabata M, Imai S, Iijima S, Kasai D, Anh TK, Fukuda MJ Biosci Bioeng10.1016/j.jbiosc.2016.11.0122017Aldehydes/chemistry/metabolism, Base Sequence, Escherichia coli/genetics, Genes, Bacterial/*genetics, Hemiterpenes/chemistry/metabolism, *Industry, Latex/chemistry/metabolism, Nocardia/classification/*genetics/*metabolism, Rubber/chemistry/*metabolism, VietnamPhylogeny
Metabolism31552514Nocardia panacis sp. nov., a novel actinomycete with antiphytopathogen activity isolated from the rhizosphere of Panax notoginseng.Hu JY, Li L, Peng G, Li YQ, Xu LH, Guan HL, Zhao LX, Miao CPAntonie Van Leeuwenhoek10.1007/s10482-019-01326-z2019Actinobacteria/*drug effects, Base Composition/genetics/physiology, Cardiolipins/metabolism, DNA, Bacterial/metabolism, Nocardia, Panax notoginseng/*chemistry, Phosphatidylethanolamines/metabolism, Phosphatidylinositols/metabolism, Phylogeny, Plant Extracts/chemistry/*pharmacology, RNA, Ribosomal, 16S/metabolism, *Rhizosphere, Soil Microbiology, Vitamin K 2/metabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11231Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43665)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43665
18497Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43665.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
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
68371Automatically annotated from API 50CH acid
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
79939Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID70749.1StrainInfo: A central database for resolving microbial strain identifiers
119283Curators of the CIPCollection of Institut Pasteur (CIP 104775)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104775