Strain identifier
BacDive ID: 11222
Type strain:
Species: Nocardiopsis chromatogenes
Strain history: <- WJ Li, Yunnan Univ.
NCBI tax ID(s): 1246475 (strain), 280239 (species)
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 id | Matching level |
---|---|
280239 | species |
1246475 | strain |
strain history
@ref | history |
---|---|
12025 | <- W.-J. Li, YIM |
67770 | KCTC 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
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
31676 | positive | rod-shaped | no | |
67771 | positive | |||
69480 | positive | 100 |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19880 | Red brown | 10-14 days | ISP 2 |
19880 | Brown beige | 10-14 days | ISP 3 |
19880 | Brown beige | 10-14 days | ISP 4 |
19880 | Brown beige | 10-14 days | ISP 5 |
19880 | Brown beige | 10-14 days | ISP 6 |
19880 | Brown beige | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
19880 | no | ISP 2 |
19880 | no | ISP 3 |
19880 | no | ISP 4 |
19880 | no | ISP 5 |
19880 | no | ISP 6 |
19880 | no | ISP 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
@ref | name | growth | link | composition |
---|---|---|---|---|
12025 | GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159) | yes | https://mediadive.dsmz.de/medium/1159 | Name: 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 |
12025 | MODIFIED ISP5 MEDIUM WITH SODIUM CHLORIDE (DSMZ Medium 993c) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium993c.pdf | |
19880 | ISP 2 | yes | Name: 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 | |
19880 | ISP 3 | yes | Name: 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: | |
19880 | ISP 4 | yes | Name: 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 | |
19880 | ISP 5 | yes | Name: 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 | |
19880 | ISP 6 | yes | Name: 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 | |
19880 | ISP 7 | yes | Name: 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 | |
12025 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://mediadive.dsmz.de/medium/553 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
12025 | positive | growth | 28 | mesophilic |
19880 | positive | optimum | 28 | mesophilic |
31676 | positive | growth | 20-60 | |
31676 | positive | optimum | 37-40 | |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31676 | positive | growth | 06-09 | alkaliphile |
31676 | positive | optimum | 7.2 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31676 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31676 | yes | |
69481 | yes | 100 |
69480 | yes | 99.999 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
19880 | NaCl | positive | maximum | 10 % |
31676 | NaCl | positive | growth | 0-18 % |
31676 | NaCl | positive | optimum | 05-08 % |
observation
@ref | observation |
---|---|
31676 | aggregates in chains |
67770 | quinones: MK-10, MK-10(H2), MK-10(H4) |
67771 | quinones: MK-10, MK-10(H2), MK-10(H4) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
19880 | 17234 | glucose | + | |
19880 | 22599 | arabinose | + | |
19880 | 17992 | sucrose | + | |
19880 | 18222 | xylose | - | |
19880 | 17268 | myo-inositol | + | |
19880 | 29864 | mannitol | + | |
19880 | 28757 | fructose | + | |
19880 | 26546 | rhamnose | + | |
19880 | 16634 | raffinose | - | |
19880 | 62968 | cellulose | - | |
31676 | 22599 | arabinose | + | carbon source |
31676 | 17057 | cellobiose | + | carbon source |
31676 | 28757 | fructose | + | carbon source |
31676 | 28260 | galactose | + | carbon source |
31676 | 17234 | glucose | + | carbon source |
31676 | 17754 | glycerol | + | carbon source |
31676 | 17716 | lactose | + | carbon source |
31676 | 17306 | maltose | + | carbon source |
31676 | 29864 | mannitol | + | carbon source |
31676 | 37684 | mannose | + | carbon source |
31676 | 16634 | raffinose | + | carbon source |
31676 | 26546 | rhamnose | + | carbon source |
31676 | 33942 | ribose | + | carbon source |
31676 | 17992 | sucrose | + | carbon source |
31676 | 18222 | xylose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19880 | + | + | + | - | + | - | - | - | + | + | - | - | + | - | + | + | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
12025 | hypersaline soil | Xin Jiang Province | China | CHN | Asia |
67770 | Saline soil | China | CHN | Asia | |
67771 | hypersaline soils in Xinjiang province | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
12025 | 1 | Risk group (German classification) |
19880 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardiopsis chromatogenes YIM 90109 | 1246475.3 | wgs | patric | 1246475 |
66792 | Nocardiopsis chromatogenes YIM 90109 | 2551306678 | draft | img | 1246475 |
67770 | Nocardiopsis chromatogenes YIM 90109 | GCA_000341185 | contig | ncbi | 1246475 |
GC content
@ref | GC-content | method |
---|---|---|
12025 | 71.8 | |
67770 | 71.8 | thermal denaturation, midpoint method (Tm) |
67770 | 73.8 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 91.032 | yes |
gram-positive | yes | 90.655 | yes |
anaerobic | no | 99.183 | yes |
aerobic | yes | 92.557 | no |
halophile | yes | 64.679 | no |
spore-forming | yes | 92.743 | no |
glucose-util | yes | 87.238 | yes |
flagellated | no | 98.25 | yes |
thermophile | no | 96.948 | yes |
glucose-ferment | no | 89.777 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16627660 | Five 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 CL | Int J Syst Evol Microbiol | 10.1099/ijs.0.64033-0 | 2006 | Actinomycetales/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 & purification | Enzymology |
Pathogenicity | 27484832 | Two new sesquiterpenoids produced by halophilic Nocardiopsis chromatogenes YIM 90109. | Sun MW, Zhang XM, Bi HL, Li WJ, Lu CH | Nat Prod Res | 10.1080/14786419.2016.1214831 | 2016 | Actinomycetales/*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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
12025 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44844) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44844 | |||
19880 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44844.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31676 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27954 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
80465 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134264.1 | StrainInfo: A central database for resolving microbial strain identifiers |