Strain identifier

BacDive ID: 11236

Type strain: Yes

Species: Nocardiopsis kunsanensis

Strain history: <- X-L Cui, Yunnan Inst., China

NCBI tax ID(s): 141693 (species)

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General

@ref: 15477

BacDive-ID: 11236

DSM-Number: 45168

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

description: Nocardiopsis kunsanensis DSM 45168 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sea anemone collected from a tidal flat.

NCBI tax id

  • NCBI tax id: 141693
  • Matching level: species

strain history

@refhistory
15477<- X.-L. Cui, YIM; JSM 073097 <- Y.-G. Chen and et al.
67770KCTC 19473 <-- Y.-G. Chen et al. JSM 073097.
67771<- X-L Cui, Yunnan Inst., China

doi: 10.13145/bacdive11236.20230509.8.1

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: 15477

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis litoralis

full scientific name: Nocardiopsis litoralis Chen et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29257positive1.65 µm0.6 µmrod-shapedno
67771positive
69480no90.999
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
20172Grey white (9002)10-14 daysISP 2
20172Grey white (9002)10-14 daysISP 3
2017210-14 daysISP 4
2017210-14 daysISP 5
2017210-14 daysISP 6
2017210-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20172noISP 2
20172noISP 3
20172noISP 4
20172noISP 5
20172noISP 6
20172noISP 7

pigmentation

  • @ref: 29257
  • production: yes

multimedia

  • @ref: 15477
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45168.jpg
  • caption: Medium 514 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15477BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
20172ISP 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
20172ISP 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:
20172ISP 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
20172ISP 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
20172ISP 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
20172ISP 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
15477positivegrowth28mesophilic
20172positiveoptimum28mesophilic
29257positivegrowth20-35
29257positiveoptimum25mesophilic
67770positivegrowth25mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29257positivegrowth6-10.5alkaliphile
29257positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29257aerobe
67771aerobe

spore formation

@refspore formationconfidence
29257yes
69480yes99.476

halophily

@refsaltgrowthtested relationconcentration
29257NaClpositivegrowth01-15 %
29257NaClpositiveoptimum6 %

observation

@refobservation
29257aggregates in chains
67770quinones: MK-10(H4), MK-10(H6), MK-10(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2017217234glucose+
2017222599arabinose+
2017217992sucrose+
2017218222xylose+
2017217268myo-inositol+/-
2017229864mannitol+/-
2017228757fructose+
2017226546rhamnose+
2017216634raffinose+
2017262968cellulose+/-
2925716449alanine+carbon source
2925717234glucose+carbon source
2925717992sucrose+carbon source
2925718222xylose+carbon source

enzymes

@refvalueactivityec
29257catalase+1.11.1.6
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
20172+++-++--+++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15477sea anemone collected from a tidal flatSouth China Sea, Naozhou Island, near Zhanjiang CityChinaCHNAsia
67771From sea waterGuangdong ProvinceChinaCHNAsia
67770Homogenates of a sea anemone from a tidal flat on Naozhou Island in the South China Seanear Zhanjiang City, southern ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Tidal flat
#Host#Invertebrates (Other)#Cnidaria (Corals)

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: EU583726
  • Sequence Identity:
  • Total samples: 497
  • soil counts: 82
  • aquatic counts: 28
  • animal counts: 376
  • plant counts: 11

Safety information

risk assessment

  • @ref: 15477
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15477
  • description: Nocardiopsis litoralis strain JSM 073097 16S ribosomal RNA gene, partial sequence
  • accession: EU583726
  • length: 1404
  • database: ena
  • NCBI tax ID: 516701

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis kunsanensis KCTC 19473GCA_014651735scaffoldncbi141693
66792Nocardiopsis litoralis strain KCTC 19473516701.3wgspatric516701

GC content

@refGC-contentmethod
1547770.4high performance liquid chromatography (HPLC)
2925770.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes78no
flagellatedno97.995yes
gram-positiveyes91.876yes
anaerobicno99.492yes
aerobicyes93.73yes
halophileyes82.609yes
spore-formingyes91.558no
glucose-utilyes91.136no
thermophileno96.333no
motileno93.264yes
glucose-fermentno91.275no

External links

@ref: 15477

culture collection no.: DSM 45168, KCTC 19473, JSM 073097, JCM 16954

straininfo link

  • @ref: 80471
  • straininfo: 401800

literature

  • topic: Phylogeny
  • Pubmed-ID: 19625431
  • title: Nocardiopsis litoralis sp. nov., a halophilic marine actinomycete isolated from a sea anemone.
  • authors: Chen YG, Wang YX, Zhang YQ, Tang SK, Liu ZX, Xiao HD, Xu LH, Cui XL, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.009704-0
  • year: 2009
  • mesh: Actinomycetales/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/*metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15477Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45168)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45168
20172Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45168.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
29257Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2567628776041
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
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)
80471Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401800.1StrainInfo: A central database for resolving microbial strain identifiers