Strain identifier

BacDive ID: 10799

Type strain: Yes

Species: Nocardia concava

Strain history: CIP <- 2005, DSMZ <- Y. Mikami <- IFM

NCBI tax ID(s): 1206741 (strain), 257281 (species)

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General

@ref: 11991

BacDive-ID: 10799

DSM-Number: 44804

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

description: Nocardia concava DSM 44804 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from human.

NCBI tax id

NCBI tax idMatching level
1206741strain
257281species

strain history

@refhistory
11991<- Y. Mikami, IFM
67770Y. Mikami IFM 0354.
118719CIP <- 2005, DSMZ <- Y. Mikami <- IFM

doi: 10.13145/bacdive10799.20230509.8.1

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

@ref: 11991

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia concava

full scientific name: Nocardia concava Kageyama et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidencecell shape
31312positive2.25 µm2.25 µmno
69480no96.153
69480positive100
118719positivenorod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20121Lemon yellow (1012)10-14 daysISP 2
20121Lemon yellow (1012)10-14 daysISP 3
2012110-14 daysISP 4
20121Beige (1001)10-14 daysISP 5
20121Lemon yellow (1012)10-14 daysISP 6
20121Brown beige (1011)10-14 daysISP 7
118719

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20121yesAerial MyceliumWhiteISP 2
20121noISP 3
20121noISP 4
20121noISP 5
20121noISP 6
20121noISP 7

pigmentation

  • @ref: 31312
  • production: yes

multimedia

  • @ref: 11991
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44804.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11991TRYPTICASE 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
20121ISP 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
20121ISP 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:
20121ISP 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
20121ISP 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
20121ISP 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
20121ISP 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
34015MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118719CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
11991positivegrowth28mesophilic
20121positiveoptimum28mesophilic
31312positivegrowth37-44
31312positiveoptimum37mesophilic
34015positivegrowth30mesophilic
59483positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31312aerobe
59483aerobe
118719obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480no97.908

observation

@refobservation
31312aggregates in clumps
67770quinones: MK-9(H4, ω-cycl)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2012117234glucose+
2012122599arabinose+
2012117992sucrose+
2012118222xylose-
2012117268myo-inositol+
2012129864mannitol+
2012128757fructose+
2012126546rhamnose-
2012116634raffinose-
2012162968cellulose-
3131222599arabinose+carbon source
3131216947citrate+carbon source
3131228260galactose+carbon source
3131217234glucose+carbon source
3131237684mannose+carbon source
11871917632nitrate+reduction
11871916301nitrite-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917992sucrose-fermentation

metabolite production

  • @ref: 118719
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31312urease+3.5.1.5
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
118719oxidase-
118719alcohol dehydrogenase-1.1.1.1
118719catalase+1.11.1.6
118719lysine decarboxylase-4.1.1.18
118719ornithine decarboxylase-4.1.1.17
118719urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
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-fucosidase-3.2.1.51

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
20121+++--+--++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20121++++++-+-++---++-+-
118719+++-+----++---++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11991humanJapanJPNAsia
67770Japanese patient
118719HumanJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119912Risk group (German classification)
201212German classification
1187192Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia concava strain DSM 44804 16S ribosomal RNA gene, partial sequenceEF1774641461ena257281
20218Nocardia concava 16S ribosomal RNA gene, partial sequenceGQ3761641439ena257281
31312Nocardia concava gene for 16S rRNA, partial sequence, strain:IFM 0354AB1268801472nuccore257281

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia concava NBRC 1004301206741.4wgspatric1206741
66792Nocardia concava NBRC 1004302551306180draftimg1206741
67770Nocardia concava NBRC 100430GCA_000308815contigncbi1206741

GC content

@refGC-contentmethod
1199167-68
3131267.5
6777067.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno91.197no
gram-positiveyes88.482no
anaerobicno99.52yes
aerobicyes82.07yes
halophileno94.508no
spore-formingyes82.129no
glucose-utilyes91.565yes
flagellatedno97.617yes
thermophileno99.651yes
glucose-fermentno87.986no

External links

@ref: 11991

culture collection no.: DSM 44804, CIP 108975, IFM 0354, JCM 12351, NBRC 100430, CCUG 52242

straininfo link

  • @ref: 80064
  • straininfo: 215504

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166713Nocardia concava sp. nov., isolated from Japanese patients.Kageyama A, Yazawa K, Taniguchi H, Chibana H, Nishimura K, Kroppenstedt RM, Mikami YInt J Syst Evol Microbiol10.1099/ijs.0.63280-02005Bacterial Typing Techniques, DNA, Bacterial, DNA, Ribosomal, Genes, rRNA, Humans, Japan, Molecular Sequence Data, Nocardia/*classification/genetics/*isolation & purification/physiology, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNAPathogenicity
Phylogeny27255509Nocardia shinanonensis sp. nov., isolated from a patient with endophthalmitis.Matsumoto T, Negishi T, Hamada M, Komaki H, Gonoi T, Yaguchi TInt J Syst Evol Microbiol10.1099/ijsem.0.0011972016Aqueous Humor/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Endophthalmitis/*microbiology, Fatty Acids/chemistry, Humans, Mycolic Acids/chemistry, Nocardia/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny28875906Nocardia heshunensis sp. nov., an actinomycete isolated from soil.Huang JR, Ming H, Duan YY, Li S, Zhang LY, Ji WL, Zhao ZL, Meng XL, Li WJ, Nie GXInt J Syst Evol Microbiol10.1099/ijsem.0.0021432017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Mycolic Acids/chemistry, Nocardia/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31339486Nocardia yunnanensis sp. nov., an actinomycete isolated from a soil sample.Zhang JX, Ming H, Zhao ZL, Ji WL, Chang XL, Zhang LY, Cheng LJ, Meng XL, Li WJ, Nie GXInt J Syst Evol Microbiol10.1099/ijsem.0.0036002019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nocardia/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33146799Nocardia terrae sp. nov., an actinomycete isolated from soil in Thailand.Kanchanasin P, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Tanasupawat SArch Microbiol10.1007/s00203-020-02107-32020Base Composition, Fatty Acids/chemistry, Nocardia/*classification/genetics/isolation & purification, Phospholipids/chemistry, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity, ThailandEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
11991Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44804)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44804
20121Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44804.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
31312Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127627
34015Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6664
59483Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52242)https://www.ccug.se/strain?id=52242
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
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
80064Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID215504.1StrainInfo: A central database for resolving microbial strain identifiers
118719Curators of the CIPCollection of Institut Pasteur (CIP 108975)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108975