Strain identifier

BacDive ID: 11222

Type strain: Yes

Species: Nocardiopsis chromatogenes

Strain history: <- WJ Li, Yunnan Univ.

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

@ref: 12025

BacDive-ID: 11222

DSM-Number: 44844

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

description: Nocardiopsis chromatogenes DSM 44844 is an aerobe, spore-forming, mesophilic bacterium that was isolated from hypersaline soil.

NCBI tax id

NCBI tax idMatching level
280239species
1246475strain

strain history

@refhistory
12025<- W.-J. Li, YIM
67770KCTC 19008 <-- W.-J. Li YIM 90109.
67771<- WJ Li, Yunnan Univ.

doi: 10.13145/bacdive11222.20230509.8.1

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 chromatogenes
  • full scientific name: Nocardiopsis chromatogenes Li et al. 2006

@ref: 12025

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis chromatogenes

full scientific name: Nocardiopsis chromatogenes Li et al. 2006 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31676positiverod-shapedno
67771positive
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19880Red brown10-14 daysISP 2
19880Brown beige10-14 daysISP 3
19880Brown beige10-14 daysISP 4
19880Brown beige10-14 daysISP 5
19880Brown beige10-14 daysISP 6
19880Brown beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19880noISP 2
19880noISP 3
19880noISP 4
19880noISP 5
19880noISP 6
19880noISP 7

pigmentation

  • @ref: 31676
  • production: yes

multimedia

  • @ref: 12025
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44844.jpg
  • caption: Medium 1159 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12025GYM 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
12025MODIFIED ISP5 MEDIUM WITH SODIUM CHLORIDE (DSMZ Medium 993c)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium993c.pdf
19880ISP 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
19880ISP 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:
19880ISP 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
19880ISP 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
19880ISP 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
19880ISP 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
12025GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
12025positivegrowth28mesophilic
19880positiveoptimum28mesophilic
31676positivegrowth20-60
31676positiveoptimum37-40
67770positivegrowth28mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31676positivegrowth06-09alkaliphile
31676positiveoptimum7.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31676aerobe
67771aerobe

spore formation

@refspore formationconfidence
31676yes
69481yes100
69480yes99.999

halophily

@refsaltgrowthtested relationconcentration
19880NaClpositivemaximum10 %
31676NaClpositivegrowth0-18 %
31676NaClpositiveoptimum05-08 %

observation

@refobservation
31676aggregates in chains
67770quinones: MK-10, MK-10(H2), MK-10(H4)
67771quinones: MK-10, MK-10(H2), MK-10(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1988017234glucose+
1988022599arabinose+
1988017992sucrose+
1988018222xylose-
1988017268myo-inositol+
1988029864mannitol+
1988028757fructose+
1988026546rhamnose+
1988016634raffinose-
1988062968cellulose-
3167622599arabinose+carbon source
3167617057cellobiose+carbon source
3167628757fructose+carbon source
3167628260galactose+carbon source
3167617234glucose+carbon source
3167617754glycerol+carbon source
3167617716lactose+carbon source
3167617306maltose+carbon source
3167629864mannitol+carbon source
3167637684mannose+carbon source
3167616634raffinose+carbon source
3167626546rhamnose+carbon source
3167633942ribose+carbon source
3167617992sucrose+carbon source
3167618222xylose+carbon source

enzymes

@refvalueactivityec
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
19880+++-+---++--+-+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12025hypersaline soilXin Jiang ProvinceChinaCHNAsia
67770Saline soilChinaCHNAsia
67771hypersaline soils in Xinjiang provinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_24632.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_2754;97_3390;98_4275;99_24632&stattab=map
  • Last taxonomy: Nocardiopsis chromatogenes
  • 16S sequence: AY619715
  • Sequence Identity:
  • Total samples: 9
  • soil counts: 4
  • animal counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120251Risk group (German classification)
198801Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12025
  • description: Nocardiopsis chromatogenes 16S ribosomal RNA gene, partial sequence
  • accession: AY619715
  • length: 1438
  • database: ena
  • NCBI tax ID: 1246475

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis chromatogenes YIM 901091246475.3wgspatric1246475
66792Nocardiopsis chromatogenes YIM 901092551306678draftimg1246475
67770Nocardiopsis chromatogenes YIM 90109GCA_000341185contigncbi1246475

GC content

@refGC-contentmethod
1202571.8
6777071.8thermal denaturation, midpoint method (Tm)
6777073.8genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno91.032yes
gram-positiveyes90.655yes
anaerobicno99.183yes
aerobicyes92.557no
halophileyes64.679no
spore-formingyes92.743no
glucose-utilyes87.238yes
flagellatedno98.25yes
thermophileno96.948yes
glucose-fermentno89.777no

External links

@ref: 12025

culture collection no.: DSM 44844, CCTCC AA 2040015, CIP 109297, KCTC 19008, NBRC 104398, YIM 90109, JCM 15311

straininfo link

  • @ref: 80465
  • straininfo: 134264

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16627660Five novel species of the genus Nocardiopsis isolated from hypersaline soils and emended description of Nocardiopsis salina Li et al. 2004.Li WJ, Kroppenstedt RM, Wang D, Tang SK, Lee JC, Park DJ, Kim CJ, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.64033-02006Actinomycetales/chemistry/*classification/cytology/genetics/*isolation & purification, Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Growth Inhibitors/pharmacology, Lipids/analysis/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride/pharmacology, *Soil Microbiology, Vitamin K 2/analysis/isolation & purificationEnzymology
Pathogenicity27484832Two new sesquiterpenoids produced by halophilic Nocardiopsis chromatogenes YIM 90109.Sun MW, Zhang XM, Bi HL, Li WJ, Lu CHNat Prod Res10.1080/14786419.2016.12148312016Actinomycetales/*chemistry, Anti-Infective Agents/*chemistry/*pharmacology, Bacteria/drug effects, Fermentation, Fungi/drug effects, Magnetic Resonance Spectroscopy, Models, Molecular, Sesquiterpenes/*chemistry/*pharmacology, Spectrometry, Mass, Electrospray Ionization, X-Ray Diffraction

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12025Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44844)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44844
19880Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44844.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
31676Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2795428776041
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)
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
80465Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134264.1StrainInfo: A central database for resolving microbial strain identifiers