Strain identifier
BacDive ID: 11100
Type strain: 
Species: Nocardioides simplex
Strain history: CIP <- 1982, ATCC <- NCTC, Corynebacterium simplex <- H.L. Jensen
NCBI tax ID(s): 2045 (species)
version 8.1 (current version)
General
@ref: 8555
BacDive-ID: 11100
DSM-Number: 20130
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Nocardioides simplex CCUG 23611 is a mesophilic bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 2045
- Matching level: species
strain history
| @ref | history |
|---|---|
| 8555 | <- NCIB <- NCTC <- H.L. Jensen (Corynebacterium simplex) |
| 67770 | K. Suzuki CNF 035 <-- AJ 1420 <-- ATCC 6946 <-- NCTC 4215 <-- H. L. Jensen. |
| 122620 | CIP <- 1982, ATCC <- NCTC, Corynebacterium simplex <- H.L. Jensen |
doi: 10.13145/bacdive11100.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Nocardioidaceae
- genus: Nocardioides
- species: Nocardioides simplex
- full scientific name: Nocardioides simplex (Jensen 1934) O'Donnell et al. 1983
synonyms
@ref synonym 20215 Arthrobacter simplex 20215 Corynebacterium simplex 20215 Pimelobacter simplex
@ref: 8555
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides simplex
full scientific name: Nocardioides simplex (Jensen 1934) O'Donnell et al. 1983 emend. Nouioui et al. 2018
type strain: yes
Morphology
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 18625 | Colorless | 10-14 days | ISP 2 |
| 18625 | Colorless | 10-14 days | ISP 3 |
| 18625 | Colorless | 10-14 days | ISP 4 |
| 18625 | Colorless | 10-14 days | ISP 5 |
| 18625 | Colorless | 10-14 days | ISP 6 |
| 18625 | Colorless | 10-14 days | ISP 7 |
multicellular morphology
| @ref | forms multicellular complex | medium name |
|---|---|---|
| 18625 | no | ISP 2 |
| 18625 | no | ISP 3 |
| 18625 | no | ISP 4 |
| 18625 | no | ISP 5 |
| 18625 | no | ISP 6 |
| 18625 | no | ISP 7 |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 8555 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
| 18625 | 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 | |
| 18625 | 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: | |
| 18625 | 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 | |
| 18625 | 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 | |
| 18625 | 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 | |
| 18625 | 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 | |
| 37734 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
| 8555 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
| 122620 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 8555 | positive | growth | 28 | mesophilic |
| 37734 | positive | growth | 25 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
compound production
| @ref | compound |
|---|---|
| 8555 | steroids, 7-cyano |
| 8555 | pregnadienes |
| 8555 | 5' nucleotides |
| 8555 | dienes |
| 8555 | steroids, 3-ketoDelta1,4 |
murein
- @ref: 8555
- murein short key: A41.01
- type: A3gamma LL-Dpm-Gly
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
Isolation, sampling and environmental information
isolation
| @ref | sample type |
|---|---|
| 8555 | soil |
| 47831 | Rice soil |
| 67770 | Soil |
| 122620 | Environment, Rice soil |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_6659.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_452;97_518;98_4911;99_6659&stattab=map
- Last taxonomy: Pimelobacter simplex
- 16S sequence: Z78212
- Sequence Identity:
- Total samples: 374
- soil counts: 197
- aquatic counts: 68
- animal counts: 61
- plant counts: 48
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 8555 | 1 | Risk group (German classification) |
| 18625 | 1 | Hazard group |
| 122620 | 1 | Risk group (French classification) |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Nocardioides simplex 16S ribosomal RNA gene, partial sequence | AF005013 | 1474 | ena | 2045 |
| 20218 | Nocardioides simplex strain ATCC 15799 16S-23S internal transcribed spacer, complete sequence | AF017499 | 386 | ena | 2045 |
| 20218 | N.simplex 16S rRNA gene | Z78212 | 1468 | ena | 2045 |
| 20218 | Pimelobacter simplex strain KCTC 9106 16S ribosomal RNA gene, partial sequence | AF005009 | 1474 | ena | 2045 |
| 20218 | Nocardioides simplex strain KCTC 9106 16S-23S internal transcribed spacer, complete sequence | AF017494 | 386 | ena | 2045 |
| 20218 | Nocardioides simplex partial 16S rRNA | X53213 | 1392 | ena | 2045 |
| 67770 | Arthobacter simplex small subunit ribosomal RNA | M37693 | 1517 | ena | 2045 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pimelobacter simplex strain ATCC 6946 | 2045.9 | wgs | patric | 2045 |
| 66792 | Pimelobacter simplex strain NBRC 12069 | 2045.10 | wgs | patric | 2045 |
| 66792 | Pimelobacter simplex ATCC 6946 | 2687453782 | draft | img | 2045 |
| 67770 | Pimelobacter simplex NBRC 12069 | GCA_006538965 | contig | ncbi | 2045 |
| 67770 | Pimelobacter simplex ATCC 6946 | GCA_900114845 | scaffold | ncbi | 2045 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8555 | 71.7 | |
| 67770 | 71.7 | thermal denaturation, midpoint method (Tm) |
| 67770 | 73 | thermal denaturation, midpoint method (Tm) |
| 67770 | 74 | |
| 67770 | 74.4 | thermal denaturation, midpoint method (Tm) |
| 67770 | 72.9 | genome sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 75.699 | no |
| gram-positive | yes | 88.972 | no |
| anaerobic | no | 98.281 | no |
| aerobic | yes | 87.789 | no |
| halophile | no | 95.352 | no |
| spore-forming | no | 73.928 | no |
| glucose-util | yes | 84.458 | no |
| flagellated | no | 92.699 | no |
| thermophile | no | 98.396 | yes |
| glucose-ferment | no | 88.964 | no |
External links
@ref: 8555
culture collection no.: CCUG 23611, JCM 1363, DSM 20130, ATCC 6946, CCM 1652, DSM 776, IAM 1660, IMET 10368, NCIB 8929, NCTC 4215, BCRC 10381, CECT 466, CIP 82.106, HAMBI 1861, HAMBI 90, IFO 12069, IFO 3530, IMSNU 21329, KCTC 1003, KCTC 3187, KCTC 9106, LMG 16261, NBRC 12069, NBRC 3530, NCCB 39010, NCIMB 8929, NRIC 1841, NRRL B-14051, NRRL B-3157, PCM 2327, VKM Ac-1118, VKM Ac-925, VKM B-667
straininfo link
- @ref: 80349
- straininfo: 88162
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 1366455 | The use of free and immobilised Arthrobacter simplex in organic solvent/aqueous two-liquid-phase reactors. | Hocknull MD, Lilly MD | Appl Microbiol Biotechnol | 10.1007/BF00176516 | 1990 | Arthrobacter/*metabolism, Hydrocortisone/*metabolism, Kinetics, Solvents | Enzymology |
| Metabolism | 1367800 | Delta'-dehydrogenation of steroids by Arthrobacter simplex immobilized in calcium polygalacturonate beads. | Montes MC, Magana I | J Ind Microbiol | 10.1007/BF01576064 | 1991 | Arthrobacter/enzymology/*metabolism, Cortodoxone/*metabolism, Hydrocortisone/*metabolism, Hydrogen-Ion Concentration, Hydroxysteroid Dehydrogenases/*metabolism, Microspheres, Oxygen/metabolism, Pectins, Prednisolone/analysis/metabolism, Vitamin K/metabolism | Enzymology |
| Enzymology | 8586617 | Purification and characterization of the 3-ketosteroid-delta 1-dehydrogenase of Arthrobacter simplex produced in Streptomyces lividans. | Choi KP, Molnar I, Yamashita M, Murooka Y | J Biochem | 10.1093/oxfordjournals.jbchem.a124804 | 1995 | Amino Acid Sequence, Arthrobacter/*enzymology, Chromatography, High Pressure Liquid, Conserved Sequence, Extracellular Matrix/enzymology, Hydrogen-Ion Concentration, Molecular Sequence Data, Oxidoreductases/*chemistry/*isolation & purification/physiology, Sequence Homology, Amino Acid, Steroids/metabolism, Streptomyces/*enzymology, Substrate Specificity, Temperature | Genetics |
| Phylogeny | 8757942 | Mineralization of 2,4,6-trinitrophenol (picric acid): characterization and phylogenetic identification of microbial strains. | Rajan J, Valli K, Perkins RE, Sariaslani FS, Barns SM, Reysenbach AL, Rehm S, Ehringer M, Pace NR | J Ind Microbiol | 10.1007/BF01570041 | 1996 | Base Sequence, Biodegradation, Environmental, Fatty Acids/analysis, Gram-Positive Bacteria/genetics/isolation & purification/*metabolism, Industrial Waste, Molecular Sequence Data, Phylogeny, Picrates/*metabolism, Species Specificity | Metabolism |
| Enzymology | 10930735 | Purification and characterization of histamine dehydrogenase from Nocardioides simplex IFO 12069. | Siddiqui JA, Shoeb SM, Takayama S, Shimizu E, Yorifuji T | FEMS Microbiol Lett | 10.1111/j.1574-6968.2000.tb09227.x | 2000 | Amine Oxidase (Copper-Containing)/*isolation & purification/*metabolism, Catalysis, Nocardiaceae/*enzymology, Substrate Specificity | Phylogeny |
| Metabolism | 11867272 | Conversion of liposomal 4-androsten-3,17-dione by A. simplex immobilized cells in calcium pectate. | Llanes N, Pendas J, Falero A, Perez C, Hung BR, Moreira T | J Steroid Biochem Mol Biol | 10.1016/s0960-0760(01)00176-5 | 2002 | Androstenedione/*metabolism, Arthrobacter/*metabolism, Liposomes/*chemistry/metabolism, Pectins/*metabolism, Solutions/chemistry, Water/chemistry/metabolism | |
| Metabolism | 17936614 | Enhancement of androstadienedione production from progesterone by biotransformation using the hydroxypropyl-beta-cyclodextrin complexation technique. | Manosroi A, Saowakhon S, Manosroi J | J Steroid Biochem Mol Biol | 10.1016/j.jsbmb.2007.05.032 | 2007 | 2-Hydroxypropyl-beta-cyclodextrin, Androstenedione/*analogs & derivatives/*metabolism, Bacillus/metabolism, Bacteriological Techniques, Biotransformation/drug effects, Excipients/pharmacology, Progesterone/*pharmacokinetics, beta-Cyclodextrins/*pharmacology | Biotechnology |
| 18597329 | Ultrasound-enhanced bioprocess. II: Dehydrogenation of hydrocortisone by Arthrobacter simplex. | Zabaneh M, Bar R | Biotechnol Bioeng | 10.1002/bit.260371103 | 1991 | |||
| Phylogeny | 19625430 | Nocardioides humi sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field. | Kim MK, Srinivasan S, Park MJ, Sathiyaraj G, Kim YJ, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.008821-0 | 2009 | Actinomycetales/classification/enzymology/genetics/*isolation & purification, Bacterial Proteins/*metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, *Panax, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, beta-Glucosidase/*metabolism | Metabolism |
| Phylogeny | 19628618 | Nocardioides caeni sp. nov., isolated from wastewater. | Yoon JH, Kang SJ, Park S, Kim W, Oh TK | Int J Syst Evol Microbiol | 10.1099/ijs.0.010124-0 | 2009 | Actinomycetales/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, *Water Microbiology | Metabolism |
| Metabolism | 23973392 | Increased yield of biotransformation of exemestane with beta-cyclodextrin complexation technique. | Li G, Li F, Deng L, Fang X, Zou H, Xu K, Li T, Tan G | Steroids | 10.1016/j.steroids.2013.07.009 | 2013 | 2-Hydroxypropyl-beta-cyclodextrin, Androstadienes/*chemistry/*metabolism, Antineoplastic Agents/*chemistry/*metabolism, Arthrobacter/metabolism, Biotransformation, Solubility, Water/chemistry, beta-Cyclodextrins/*chemistry | Biotechnology |
| Phylogeny | 24846051 | Nocardioides soli sp. nov., a bacterium isolated from a mountain soil. | Srinivasan S, Lee SS, Lee JJ, Kim MK | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0191-7 | 2014 | Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Humans, Hydrogen-Ion Concentration, Korea, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, Vitamin K 2/analysis | Pathogenicity |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8555 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20130) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20130 | |||
| 18625 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM20130.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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 37734 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/11383 | ||||
| 47831 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 23611) | https://www.ccug.se/strain?id=23611 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 80349 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID88162.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 122620 | Curators of the CIP | Collection of Institut Pasteur (CIP 82.106) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.106 |