Strain identifier

BacDive ID: 11193

Type strain: Yes

Species: Nocardiopsis lucentensis

Strain Designation: A5-1

Strain history: DSM 44048 <-- E. A. Galinski A5-1.

NCBI tax ID(s): 1246460 (strain), 53441 (species)

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General

@ref: 11462

BacDive-ID: 11193

DSM-Number: 44048

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

description: Nocardiopsis lucentensis A5-1 is a spore-forming, Gram-positive bacterium that was isolated from salt marsch soil.

NCBI tax id

NCBI tax idMatching level
53441species
1246460strain

strain history

@refhistory
11462<- E.A. Galinski, A5-1
67770DSM 44048 <-- E. A. Galinski A5-1.

doi: 10.13145/bacdive11193.20240916.9.1

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 lucentensis
  • full scientific name: Nocardiopsis lucentensis Yassin et al. 1993

@ref: 11462

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis lucentensis

full scientific name: Nocardiopsis lucentensis Yassin et al. 1993

strain designation: A5-1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480positive90.61
6948097no

colony morphology

@refincubation periodmedium usedcolony color
1962310-14 daysISP 3
1962310-14 daysISP 5
1962310-14 daysISP 7Green

multicellular morphology

@refforms multicellular complexmedium name
19623noISP 2
19623noISP 3
19623noISP 4
19623noISP 5
19623noISP 6
19623noISP 7

multimedia

  • @ref: 11462
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44048.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11462ISP MEDIUM 2 WITH 5% NaCl (DSMZ Medium 636)yeshttps://mediadive.dsmz.de/medium/636Name: ISP MEDIUM 2 WITH 5% NaCl (DSMZ Medium 636) Composition: NaCl 50.0 g/l Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
11462GYM 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
19623ISP 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:
19623ISP 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
19623ISP 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
11462ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987; with strain-specific modifications) Composition: NaCl 30.0 g/l Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
19623positiveoptimum28
11462positivegrowth37
67770positivegrowth35

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: aerobe
  • confidence: 90.169

spore formation

@refspore descriptiontype of sporespore formationconfidence
19623Formation of spores, spore surface smoothsporeyes
69481yes100

observation

  • @ref: 67770
  • observation: quinones: MK-10(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1962317234glucose+/-
1962322599arabinose+/-
1962317992sucrose+/-
1962318222xylose+/-
1962317268myo-inositol+/-
1962329864mannitol+/-
1962328757fructose+/-
1962326546rhamnose+/-
1962316634raffinose+/-
1962362968cellulose+/-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19623+++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11462salt marsch soilAlicanteSpainESPEurope
67770Salt marsh soilAlicanteSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Salt marsh
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_4684.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_2623;99_4684&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: X97888
  • Sequence Identity:
  • Total samples: 10
  • animal counts: 9
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
114621Risk group (German classification)
196231Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: N.lucentensis 16S rRNA gene
  • accession: X97888
  • length: 1461
  • database: nuccore
  • NCBI tax ID: 1246460

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis lucentensis DSM 440481246460.3wgspatric1246460
66792Nocardiopsis lucentensis DSM 440482554235034draftimg1246460
67770Nocardiopsis lucentensis DSM 44048GCA_000341125contigncbi1246460

GC content

@refGC-contentmethod
6777071high performance liquid chromatography (HPLC)
6777071.2genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.61no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.207no
69480spore-formingspore-formingAbility to form endo- or exosporesyes88.683yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.169no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.478no
69480flagellatedmotile2+Ability to perform flagellated movementno97no

External links

@ref: 11462

culture collection no.: DSM 44048, ATCC 51300, IFO 15854, JCM 9420, NBRC 15854, BCRC 16261, CGMCC 4.2082, IMSNU 22175, VKM Ac-1962

straininfo link

  • @ref: 80442
  • straininfo: 386965

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24048863Nocardiopsis fildesensis sp. nov., an actinomycete isolated from soil.Xu S, Yan L, Zhang X, Wang C, Feng G, Li JInt J Syst Evol Microbiol10.1099/ijs.0.053595-02013Actinomycetales/*classification/genetics/isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25380720Nocardiopsis algeriensis sp. nov., an alkalitolerant actinomycete isolated from Saharan soil.Bouras N, Meklat A, Zitouni A, Mathieu F, Schumann P, Sproer C, Sabaou N, Klenk HPAntonie Van Leeuwenhoek10.1007/s10482-014-0329-72014Actinobacteria/*classification/genetics/*isolation & purification/physiology, Africa, Northern, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Spores, Bacterial/cytology, Temperature, Vitamin K 2/analysisGenetics
Pathogenicity26270803Nocarbenzoxazoles A-G, Benzoxazoles Produced by Halophilic Nocardiopsis lucentensis DSM 44048.Sun M, Zhang X, Hao H, Li W, Lu CJ Nat Prod10.1021/acs.jnatprod.5b000312015Algorithms, Anti-Bacterial Agents/chemistry/*isolation & purification/pharmacology, Antineoplastic Agents/chemistry/*isolation & purification/pharmacology, Bacillus subtilis/drug effects, Benzoxazoles/chemistry/*isolation & purification/pharmacology, Candida albicans/drug effects, Cell Line, Tumor, Drug Screening Assays, Antitumor, HeLa Cells, Hep G2 Cells, Humans, Microbial Sensitivity Tests, Molecular Structure, Mycobacterium smegmatis/drug effects, Nocardia/*chemistry, Nuclear Magnetic Resonance, Biomolecular, Pseudomonas aeruginosa/drug effects, Staphylococcus aureus/drug effectsEnzymology
26540143Two new polyketides from Nocardiopsis lucentensis DSM 44048.Sun MW, Guo ZX, Lu CHNat Prod Res10.1080/14786419.2015.11046742015Actinomycetales/*chemistry, Anti-Bacterial Agents/analysis/pharmacology, Anti-Infective Agents/*analysis/*pharmacology, Antifungal Agents/analysis/pharmacology, Fermentation, Magnetic Resonance Spectroscopy, Mass Spectrometry, Microbial Sensitivity Tests, Polyketides/*analysis/*pharmacology, Spectrometry, Mass, Electrospray Ionization
Pathogenicity30958679Synthesis, Structure Revision, and Cytotoxicity of Nocarbenzoxazole G.Kim T, Lee SA, Noh T, Choi P, Choi SJ, Song BG, Kim Y, Park YT, Huh G, Kim YJ, Ham JJ Nat Prod10.1021/acs.jnatprod.9b000722019Antibiotics, Antineoplastic/*chemistry/*pharmacology, Benzoxazoles/*chemistry/*pharmacology, Cell Line, Tumor, Cell Proliferation/drug effects, HeLa Cells, Humans, Molecular Structure, Nocardia, Nuclear Magnetic Resonance, Biomolecular

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11462Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44048)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44048
19623Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44048.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
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/
68368Automatically annotated from API 20E
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
80442Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID386965.1StrainInfo: A central database for resolving microbial strain identifiers