Strain identifier

BacDive ID: 11199

Type strain: Yes

Species: Nocardiopsis kunsanensis

Strain Designation: HA-9

Strain history: CIP <- 2003, KCTC <- JCM <- S.J. Kim: strain HA-9

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11731

BacDive-ID: 11199

DSM-Number: 44524

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

description: Nocardiopsis kunsanensis HA-9 is an aerobe, spore-forming, mesophilic bacterium that was isolated from saltern.

NCBI tax id

NCBI tax idMatching level
141693species
1246445strain

strain history

@refhistory
11731<- JCM <- KCTC <- S.-J. Kim; HA-9
67770KCTC 9831 <-- S.-J. Kim HA-9.
67771<- S-J Kim HA-9
120513CIP <- 2003, KCTC <- JCM <- S.J. Kim: strain HA-9

doi: 10.13145/bacdive11199.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis kunsanensis
  • full scientific name: Nocardiopsis kunsanensis Chun et al. 2000
  • synonyms

    • @ref: 20215
    • synonym: Nocardiopsis litoralis

@ref: 11731

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis kunsanensis

full scientific name: Nocardiopsis kunsanensis Chun et al. 2000 emend. Nouioui et al. 2018

strain designation: HA-9

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
67771positive
69480no92.115
69480positive100
120513positivenorod-shaped

colony morphology

  • @ref: 120513

multimedia

@refmultimedia contentintellectual property rightscaption
11731https://www.dsmz.de/microorganisms/photos/DSM_44524-1.jpg© Leibniz-Institut DSMZ
11731https://www.dsmz.de/microorganisms/photos/DSM_44524.jpg© Leibniz-Institut DSMZMedium 1159 37°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11731GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159)yeshttps://mediadive.dsmz.de/medium/1159Name: GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159) Composition: NaCl 100.0 g/l Agar 15.0 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
37398MEDIUM 493 - for Nocardiopsis kunsanensisyesDistilled water make up to (1000.000 ml);Sodium chloride (100.000 g);Potassium chloride (2.000 g);Magnesium sulphate heptahydrate (10.000 g);Agar (15.000 g);Yeast extract (10.000 g);Casein hydrolysate acid hydrolysed vitamine-free (1.500 g);sodium citrate
11731MODIFIED CM+YE MEDIUM (B) (DSMZ Medium 910)yeshttps://mediadive.dsmz.de/medium/910Name: MODIFIED CM+YE MEDIUM (B) (DSMZ Medium 910) Composition: NaCl 100.0 g/l Agar 15.0 g/l MgSO4 x 7 H2O 10.0 g/l Yeast extract 10.0 g/l Casamino acids 7.5 g/l Trisodium citrate x 2 H2O 3.0 g/l KCl 2.0 g/l FeSO4 x 7 H2O 0.0498 g/l Distilled water
120513CIP Medium 493yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=493

culture temp

@refgrowthtypetemperaturerange
11731positivegrowth37mesophilic
37398positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic
120513positivegrowth25-37mesophilic
120513nogrowth10psychrophilic
120513nogrowth41thermophilic
120513nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481yes92
69480yes98.946

halophily

@refsaltgrowthtested relationconcentration
120513NaClpositivegrowth8-10 %
120513NaClnogrowth0 %
120513NaClnogrowth2 %
120513NaClnogrowth4 %
120513NaClnogrowth6 %

observation

@refobservation
67770quinones: MK-10(H8), MK-10(H6), MK-9(H8), MK-9(H6)
67771quinones: MK-8 (H_6_), MK-8 (H_8_)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120513citrate-carbon source16947
120513esculin-hydrolysis4853
120513hippurate+hydrolysis606565
120513nitrate-reduction17632
120513nitrite-reduction16301

antibiotic resistance

  • @ref: 120513
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120513
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12051315688acetoin-
12051317234glucose-

enzymes

@refvalueactivityec
120513oxidase+
120513beta-galactosidase-3.2.1.23
120513alcohol dehydrogenase-1.1.1.1
120513gelatinase+
120513catalase+1.11.1.6
120513gamma-glutamyltransferase+2.3.2.2
120513lysine decarboxylase-4.1.1.18
120513ornithine decarboxylase-4.1.1.17
120513phenylalanine ammonia-lyase-4.3.1.24
120513tryptophan deaminase-
120513urease-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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120513--+++------+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120513------------------------------------------------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120513--------------------------------+--------------------------------------------+---+-----------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11731salternKunsanKorea (north), Democratic People's Republic ofPRKAsia
67770SalternKunsanRepublic of KoreaKORAsia
67771From saltern at kunsanRepublic of KoreaKORAsia
120513Environment, SalternKunsanRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Condition#Saline
#Environmental#Aquatic#Non-marine Saline and Alkaline
#Environmental#Terrestrial

taxonmaps

  • @ref: 69479
  • File name: preview.99_6051.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_1154;98_1377;99_6051&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: AB368716
  • Sequence Identity:
  • Total samples: 497
  • soil counts: 82
  • aquatic counts: 28
  • animal counts: 376
  • plant counts: 11

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117311Risk group (German classification)
1205131Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardiopsis kunsanensis gene for 16S rRNA, partial sequenceAB3687161459ena141693
11731Nocardiopsis kunsanensis HA-9T 16S ribosomal RNA gene, partial sequenceAF1954121449ena141693

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis kunsanensis DSM 445241246445.3wgspatric1246445
66792Nocardiopsis kunsanensis DSM 445242551306680draftimg1246445
67770Nocardiopsis kunsanensis DSM 44524GCA_000340965contigncbi1246445

GC content

@refGC-contentmethod
1173171
6777069.6genome sequence analysis
6777071thermal denaturation, midpoint method (Tm)
6777171.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes92no
motileno93.692no
gram-positiveyes91.178no
anaerobicno99.492no
halophileyes79.063no
spore-formingyes92.265no
thermophileno96.631no
glucose-utilyes90.972no
flagellatedno97.888no
aerobicyes93.205no
glucose-fermentno92.276no

External links

@ref: 11731

culture collection no.: DSM 44524, JCM 10721, KCTC 9831, BCRC 16383, CGMCC 4.2083, CIP 108008, NBRC 100348

straininfo link

  • @ref: 80446
  • straininfo: 50671

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11034504Nocardiopsis kunsanensis sp. nov., a moderately halophilic actinomycete isolated from a saltern.Chun J, Bae KS, Moon EY, Jung SO, Lee HK, Kim SJInt J Syst Evol Microbiol10.1099/00207713-50-5-19092000Actinomycetales/*classification/*genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Salts, Sequence Analysis, DNAGenetics
Phylogeny19625431Nocardiopsis litoralis sp. nov., a halophilic marine actinomycete isolated from a sea anemone.Chen YG, Wang YX, Zhang YQ, Tang SK, Liu ZX, Xiao HD, Xu LH, Cui XL, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.009704-02009Actinomycetales/classification/genetics/*isolation & purification/metabolism, Animals, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Anemones/*microbiology, Sodium Chloride/*metabolismMetabolism
Phylogeny20118291Nocardiopsis nikkonensis sp. nov., isolated from a compost sample.Yamamura H, Ohkubo SY, Ishida Y, Otoguro M, Tamura T, Hayakawa MInt J Syst Evol Microbiol10.1099/ijs.0.016956-02010Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics
Phylogeny34128783Nocardiopsis coralli sp. nov. a novel actinobacterium isolated from the coral Galaxea astreata.Li F, Xie Q, Zhou S, Kong F, Xu Y, Ma Q, Wu W, Huang D, Zhao Y, Huang XInt J Syst Evol Microbiol10.1099/ijsem.0.0048172021Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nocardiopsis/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11731Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44524)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44524
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
37398Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5583
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
68371Automatically annotated from API 50CH acid
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
80446Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50671.1StrainInfo: A central database for resolving microbial strain identifiers
120513Curators of the CIPCollection of Institut Pasteur (CIP 108008)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108008