Strain identifier

BacDive ID: 10820

Type strain: Yes

Species: Nocardia speluncae

Strain Designation: N2-11

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 1210094 (strain), 419477 (species)

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General

@ref: 12321

BacDive-ID: 10820

DSM-Number: 45078

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

description: Nocardia speluncae N2-11 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil inside cave.

NCBI tax id

NCBI tax idMatching level
1210094strain
419477species

strain history

@refhistory
12321<- S. D. Lee; N2-11
67770IFM 10868 <-- DSM 45078 <-- S. D. Lee N2-11 (=JBRI 2006).
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive10820.20230509.8.1

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 speluncae
  • full scientific name: Nocardia speluncae Seo et al. 2007

@ref: 12321

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia speluncae

full scientific name: Nocardia speluncae Seo et al. 2007

strain designation: N2-11

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32180positiverod-shapedno
67771positive
69480no93.111
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19911Pastel yellow10-14 daysISP 2
19911Cream10-14 daysISP 4
19911Signal yellow10-14 daysISP 6
19911Cream10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19911noISP 2
19911noISP 4
19911noISP 6
19911noISP 7

pigmentation

  • @ref: 32180
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12321TRYPTICASE 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
19911ISP 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
19911ISP 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
19911ISP 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
19911ISP 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

culture temp

@refgrowthtypetemperaturerange
12321positivegrowth28mesophilic
19911positiveoptimum28mesophilic
32180positivegrowth10-37
32180positiveoptimum30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32180positivegrowth6.1-12.1alkaliphile
32180positiveoptimum9.1

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
32180NaClpositivegrowth0-4 %
32180NaClpositiveoptimum2 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1991117234glucose+
1991122599arabinose-
1991117992sucrose-
1991118222xylose-
1991117268myo-inositol+
1991129864mannitol+
1991128757fructose-
1991126546rhamnose-
1991116634raffinose-
1991162968cellulose-
32180620642,3-butanediol+carbon source
3218030089acetate+carbon source
3218023652dextrin+carbon source
3218017234glucose+carbon source
3218025115malate+carbon source
3218017306maltose+carbon source
3218029864mannitol+carbon source
3218030031succinate+carbon source
3218017992sucrose+carbon source
3218027082trehalose+carbon source
321804853esculin+hydrolysis
3218017632nitrate+reduction

enzymes

  • @ref: 32180
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12321soil inside caveJejuRepublic of KoreaKORAsia
67770Soil at a natural caveJeju IslandRepublic of KoreaKORAsia
67771From soil inside caveJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Geologic
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_975.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_658;98_761;99_975&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: AM422449
  • Sequence Identity:
  • Total samples: 146
  • soil counts: 80
  • aquatic counts: 38
  • animal counts: 18
  • plant counts: 10

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123211Risk group (German classification)
199111Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12321
  • description: Nocardia speluncae partial 16S rRNA gene, strain N2-11T
  • accession: AM422449
  • length: 1407
  • database: ena
  • NCBI tax ID: 419477

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia speluncae NBRC 1082511210094.4wgspatric1210094
66792Nocardia speluncae strain DSM 45078419477.3wgspatric419477
66792Nocardia speluncae DSM 450782900415656draftimg419477
66792Nocardia speluncae NBRC 1082512713896924draftimg1210094
67770Nocardia speluncae NBRC 108251GCA_001613245contigncbi1210094
67770Nocardia speluncae DSM 45078GCA_012395985contigncbi419477

GC content

@refGC-contentmethod
1232166.3
3218065.9-66.7
6777065.9-66.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.277yes
gram-positiveyes87.216no
anaerobicno99.266yes
aerobicyes86.554yes
halophileno87.521no
spore-formingyes78.296no
thermophileno98.428yes
glucose-utilyes88.621yes
flagellatedno98.02yes
glucose-fermentno92.165no

External links

@ref: 12321

culture collection no.: DSM 45078, JBRI 2006, KCTC 19223, JCM 14881, IFM 10868, NBRC 108251

straininfo link

  • @ref: 80081
  • straininfo: 323261

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18048752Nocardia speluncae sp. nov., isolated from a cave.Seo JP, Yun YW, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.65085-02007Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Korea, Molecular Sequence Data, Mycolic Acids/analysis, Nocardia/chemistry/*classification/genetics/*isolation & purification, Phylogeny, Pigments, Biological/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny19196788Nocardia jinanensis sp. nov., an amicoumacin B-producing actinomycete.Sun W, Zhang YQ, Huang Y, Zhang YQ, Yang ZY, Liu ZHInt J Syst Evol Microbiol10.1099/ijs.0.002899-02009Actinobacteria/classification/genetics/metabolism, Coumarins/*metabolism, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityMetabolism
Phylogeny21551327Nocardia grenadensis sp. nov., isolated from sand of the Caribbean Sea.Kampfer P, Lodders N, Grun-Wollny I, Martin K, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.030684-02011Bacterial Typing Techniques, Benzoquinones/analysis, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, Grenada, Molecular Sequence Data, Nocardia/*classification/genetics/*isolation & purification/physiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Silicon DioxideGenetics
Phylogeny26547854Nocardia zapadnayensis sp. nov., isolated from soil.Ozdemir-Kocak F, Saygin H, Saricaoglu S, Cetin D, Potter G, Sproer C, Guven K, Isik K, Klenk HP, Sahin NAntonie Van Leeuwenhoek10.1007/s10482-015-0612-22015Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/analysis/chemistry, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Nocardia/chemistry/cytology/genetics/*isolation & purification, Nucleic Acid Hybridization, Phospholipids/analysis/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12321Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45078)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45078
19911Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45078.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
32180Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2842228776041
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
80081Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323261.1StrainInfo: A central database for resolving microbial strain identifiers