Strain identifier

BacDive ID: 10779

Type strain: Yes

Species: Nocardia arthritidis

Strain history: CIP <- 2005, DSMZ <- IFM

NCBI tax ID(s): 1210067 (strain), 228602 (species)

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General

@ref: 12049

BacDive-ID: 10779

DSM-Number: 44731

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, rod-shaped

description: Nocardia arthritidis DSM 44731 is an obligate aerobe, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from human sputum.

NCBI tax id

NCBI tax idMatching level
1210067strain
228602species

strain history

@refhistory
12049<- Y. Mikami, IFM
67770Y. Mikami IFM 10035.
116512CIP <- 2005, DSMZ <- IFM

doi: 10.13145/bacdive10779.20230509.8.1

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 arthritidis
  • full scientific name: Nocardia arthritidis Kageyama et al. 2005

@ref: 12049

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia arthritidis

full scientific name: Nocardia arthritidis Kageyama et al. 2005

type strain: yes

Morphology

cell morphology

  • @ref: 116512
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19699Yellow orange10-14 daysISP 2
1969910-14 daysISP 3
1969910-14 daysISP 4
19699Yellow orange10-14 daysISP 5
19699Yellow orange10-14 daysISP 6
19699Yellow orange10-14 daysISP 7
116512

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19699yesAerial MyceliumYellow orangeISP 2
19699yesAerial MyceliumWhiteISP 3
19699noISP 4
19699yesAerial MyceliumYellow orangeISP 5
19699yesAerial MyceliumYellow orangeISP 6
19699yesAerial MyceliumYellow orangeISP 7

multimedia

  • @ref: 12049
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44731.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12049GPHF-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
12049TRYPTICASE 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
19699ISP 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
19699ISP 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:
19699ISP 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
19699ISP 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
19699ISP 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
19699ISP 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
36766MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116512CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
12049positivegrowth28mesophilic
19699positiveoptimum28mesophilic
36766positivegrowth30mesophilic
67770positivegrowth28mesophilic
116512positivegrowth25-41
116512nogrowth10psychrophilic
116512nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116512
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116512NaClpositivegrowth0-2 %
116512NaClnogrowth4 %
116512NaClnogrowth6 %
116512NaClnogrowth8 %
116512NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1969917234glucose+
1969922599arabinose-
1969917992sucrose-
1969918222xylose-
1969917268myo-inositol-
1969929864mannitol-
1969928757fructose+
1969926546rhamnose-
1969916634raffinose-
1969962968cellulose-
11651216947citrate-carbon source
1165124853esculin+hydrolysis
116512606565hippurate+hydrolysis
11651217632nitrate+reduction
11651216301nitrite-reduction
11651217632nitrate-respiration
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

antibiotic resistance

  • @ref: 116512
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116512
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11651215688acetoin-
11651217234glucose-

enzymes

@refvalueactivityec
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
116512oxidase-
116512beta-galactosidase-3.2.1.23
116512alcohol dehydrogenase-1.1.1.1
116512gelatinase-
116512amylase-
116512DNase-
116512caseinase-3.4.21.50
116512catalase+1.11.1.6
116512tween esterase-
116512gamma-glutamyltransferase-2.3.2.2
116512lecithinase-
116512lipase-
116512lysine decarboxylase-4.1.1.18
116512ornithine decarboxylase-4.1.1.17
116512phenylalanine ammonia-lyase-4.3.1.24
116512tryptophan deaminase-
116512urease+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

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
19699--++++-----

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19699+++-+----++---++---
116512+++-+----++---++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116512-----------------------------------------------------+---------------------+--+-----------+-----+-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12049human sputumJapanJPNAsia
67770Sputum of a patient with rheumatoid arthritisJapanJPNAsia
116512Human, SputumJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_2054.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_907;98_1606;99_2054&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: AB108781
  • Sequence Identity:
  • Total samples: 7
  • soil counts: 4
  • aquatic counts: 2
  • animal counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120492Risk group (German classification)
1165122Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia arthritidis strain DSM 44731 isolate VNS37 16S ribosomal RNA gene, partial sequenceAY903619606ena228602
20218Nocardia arthritidis strain DSM 44731 16S ribosomal RNA gene, partial sequenceDQ6598961393ena228602
20218Nocardia arthritidis culture-collection CDC:W9237 16S ribosomal RNA gene, partial sequenceGQ2174941441ena228602
20218Nocardia arthritidis strain DSM 44731 16S ribosomal RNA gene, partial sequenceJN041472462ena228602
12049Nocardia arthritidis gene for 16S rRNA, partial sequenceAB1087811514ena228602

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia arthritidis NBRC 1001371210067.4wgspatric1210067
66792Nocardia arthritidis NBRC 1001372731957727draftimg1210067
67770Nocardia arthritidis NBRC 100137GCA_001612765contigncbi1210067

GC content

@refGC-contentmethod
1204968
6777068high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.375no
gram-positiveyes86.806no
anaerobicno98.93no
aerobicyes90.716no
halophileno94.092no
spore-formingyes83.976no
glucose-utilyes87.226yes
flagellatedno98.049no
thermophileno98.699yes
glucose-fermentno91.008no

External links

@ref: 12049

culture collection no.: DSM 44731, CIP 108682, IFM 10035, JCM 12120, NBRC 100137

straininfo link

  • @ref: 80045
  • straininfo: 135130

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15184406Nocardia arthritidis sp. nov., a new pathogen isolated from a patient with rheumatoid arthritis in Japan.Kageyama A, Torikoe K, Iwamoto M, Masuyama J, Shibuya Y, Okazaki H, Yazawa K, Minota S, Kroppenstedt RM, Mikami YJ Clin Microbiol10.1128/JCM.42.6.2366-2371.20042004Aged, Arthritis, Rheumatoid/*microbiology, Humans, Male, Microbial Sensitivity Tests, Nocardia/classification/drug effects/*isolation & purification, PhylogenyPathogenicity
Phylogeny20348315Nocardia niwae sp. nov., isolated from human pulmonary sources.Moser BD, Klenk HP, Schumann P, Potter G, Lasker BA, Steigerwalt AG, Hinrikson HP, Brown JMInt J Syst Evol Microbiol10.1099/ijs.0.020370-02010Adult, Aged, Aged, 80 and over, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Female, Florida, Humans, Lung/*microbiology, Male, Microbial Sensitivity Tests, Middle Aged, Molecular Sequence Data, Nocardia/*classification/drug effects/genetics/isolation & purification, Nocardia Infections/*microbiology, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny24366612Nocardia bhagyanesis sp. nov., a novel actinomycete isolated from the rhizosphere of Callistemon citrinus (Curtis), India.Vaddavalli R, Peddi S, Kothagauni SY, Linga VRAntonie Van Leeuwenhoek10.1007/s10482-013-0093-02013Actinomycetales/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Tracheophyta/*microbiologyGenetics
Phylogeny27974088Nocardia xestospongiae sp. nov., isolated from a marine sponge in the Andaman Sea.Thawai C, Rungjindamai N, Klanbut K, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0017362017Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Indian Ocean, Nocardia/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Xestospongia/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12049Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44731)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44731
19699Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44731.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
36766Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6337
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/
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
80045Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135130.1StrainInfo: A central database for resolving microbial strain identifiers
116512Curators of the CIPCollection of Institut Pasteur (CIP 108682)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108682