Strain identifier

BacDive ID: 10810

Type strain: Yes

Species: Nocardia ninae

Strain history: CIP <- 2005, F. Laurent, Claude Bernard Univ., Lyon, France: strain OFN 02.72

NCBI tax ID(s): 1210091 (strain), 356145 (species)

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General

@ref: 12137

BacDive-ID: 10810

DSM-Number: 44978

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

description: Nocardia ninae DSM 44978 is an aerobe, spore-forming, mesophilic human pathogen that builds an aerial mycelium and was isolated from a bronchial aspirate of a 53-year old patient.

NCBI tax id

NCBI tax idMatching level
1210091strain
356145species

strain history

@refhistory
12137<- P. Boiron; OFN 02.72 <- Hopital Beayed
67770IFM 10816 <-- DSM 44978 <-- P. Boiron; OFN 02.72 <-- Beaujon Hosp., Clichy, France.
121305CIP <- 2005, F. Laurent, Claude Bernard Univ., Lyon, France: strain OFN 02.72

doi: 10.13145/bacdive10810.20230509.8.1

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 ninae
  • full scientific name: Nocardia ninae Laurent et al. 2007

@ref: 12137

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia ninae

full scientific name: Nocardia ninae Laurent et al. 2007

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
31838positiveno
69480no96.755
69480positive100
121305positivenorod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19896Yellow orange10-14 daysISP 2
19896Yellow orange10-14 daysISP 3
19896Yellow orange10-14 daysISP 4
19896Yellow orange10-14 daysISP 5
19896Yellow orange10-14 daysISP 6
19896Yellow orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19896yesAerial MyceliumWhiteISP 2
19896yesAerial MyceliumWhiteISP 3
19896noISP 4
19896noISP 5
19896noISP 6
19896noISP 7

pigmentation

  • @ref: 31838
  • production: yes

multimedia

  • @ref: 12137
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44978.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12137GYM 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
19896ISP 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
19896ISP 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:
19896ISP 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
19896ISP 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
19896ISP 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
19896ISP 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
121305CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
12137positivegrowth28mesophilic
31838positivegrowth25-37mesophilic
31838positiveoptimum31mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31838
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31838yes
69481yes99

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3183822599arabinose+carbon source
3183828260galactose+carbon source
3183817234glucose+carbon source
3183817306maltose+carbon source

enzymes

@refvalueactivityec
31838catalase+1.11.1.6
31838urease+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

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19896+++-++---++-++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
12137a bronchial aspirate of a 53-year old patientHopital BeayedFranceFRAEurope
67770Bronchial aspirate from a 53-year-old patient with an asthma attackClichyFranceFRAEurope
121305Human, Bronchial aspirateClichyFranceFRAEurope2002

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Aspirate
#Host Body-Site#Oral cavity and airways#Airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_18489.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_578;97_676;98_10074;99_18489&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: JF797312
  • Sequence Identity:
  • Total samples: 78
  • soil counts: 57
  • aquatic counts: 8
  • animal counts: 13

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12137yes, in single cases1Risk group (German classification)
198962Risk group
1213052Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia ninae strain W9812 16S ribosomal RNA gene, partial sequenceGQ8530781441ena356145
20218Nocardia ninae strain DSM 44978 16S ribosomal RNA gene, partial sequenceJF7973121414ena356145
12137Nocardia ninae strain OFN 02.72 16S ribosomal RNA gene, partial sequenceDQ2356871321ena356145

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia ninae NBRC 108245GCA_007990755contigncbi1210091
66792Nocardia ninae NBRC 1082451210091.3wgspatric1210091

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
motileno92.203yes
gram-positiveyes87.582yes
anaerobicno99.424yes
aerobicyes89.6yes
halophileno95.32no
spore-formingyes90.21yes
glucose-utilyes90.845yes
flagellatedno96.922yes
thermophileno99.672yes
glucose-fermentno92.807no

External links

@ref: 12137

culture collection no.: DSM 44978, CIP 108955, OFN 02.72, JCM 14667, IFM 10816, NBRC 108245

straininfo link

  • @ref: 80074
  • straininfo: 297467

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392183Nocardia ninae sp. nov., isolated from a bronchial aspirate.Laurent F, Rodriguez-Nava V, Noussair L, Couble A, Nicolas-Chanoine MH, Boiron PInt J Syst Evol Microbiol10.1099/ijs.0.64476-02007Asthma, Bronchi/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Humans, Middle Aged, Molecular Sequence Data, Nocardia/*classification/cytology/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/geneticsPathogenicity
Phylogeny32375925Nocardia colli sp. nov., a new pathogen isolated from a patient with primary cutaneous nocardiosis.Zhou T, Wang XY, Deng DQ, Xu LH, Li XL, Guo Y, Li WH, Xie H, Zhang PL, Zhou XHInt J Syst Evol Microbiol10.1099/ijsem.0.0038562020Adult, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Female, Humans, Mycolic Acids/chemistry, Neck, Nocardia/*classification/isolation & purification, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12137Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44978)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44978
19896Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44978.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
31838Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128104
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/
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
80074Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297467.1StrainInfo: A central database for resolving microbial strain identifiers
121305Curators of the CIPCollection of Institut Pasteur (CIP 108955)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108955