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

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

NCBI tax id

NCBI tax idMatching level
228602species
1210067strain

strain history

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

doi: 10.13145/bacdive10779.20240916.9.1

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

@refgram staincell shapemotilityconfidence
116512positiverod-shapedno
69480no90
69480positive90.642

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

@refgrowthtypetemperature
12049positivegrowth28
19699positiveoptimum28
36766positivegrowth30
67770positivegrowth28
116512positivegrowth25-41
116512nogrowth10
116512nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
116512obligate aerobe
69480aerobe90.361

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 sequenceAY903619606nuccore228602
20218Nocardia arthritidis strain DSM 44731 16S ribosomal RNA gene, partial sequenceDQ6598961393nuccore228602
20218Nocardia arthritidis culture-collection CDC:W9237 16S ribosomal RNA gene, partial sequenceGQ2174941441nuccore228602
20218Nocardia arthritidis strain DSM 44731 16S ribosomal RNA gene, partial sequenceJN041472462nuccore228602
12049Nocardia arthritidis gene for 16S rRNA, partial sequenceAB1087811514nuccore228602

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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.642no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.322yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes61.904no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.361yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.3yes
69480flagellatedmotile2+Ability to perform flagellated movementno90no

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
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)
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