Strain identifier

BacDive ID: 11100

Type strain: Yes

Species: Nocardioides simplex

Strain history: K. Suzuki CNF 035 <-- AJ 1420 <-- ATCC 6946 <-- NCTC 4215 <-- H. L. Jensen.

NCBI tax ID(s): 2045 (species)

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

@ref: 8555

BacDive-ID: 11100

DSM-Number: 20130

keywords: Bacteria, 16S sequence, genome sequence, 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

doi: 10.13145/bacdive11100.20220920.7

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

    @refsynonym
    20215Arthrobacter simplex
    20215Corynebacterium simplex
    20215Pimelobacter 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

@refcolony colorincubation periodmedium used
18625Colorless10-14 daysISP 2
18625Colorless10-14 daysISP 3
18625Colorless10-14 daysISP 4
18625Colorless10-14 daysISP 5
18625Colorless10-14 daysISP 6
18625Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18625noISP 2
18625noISP 3
18625noISP 4
18625noISP 5
18625noISP 6
18625noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8555TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://bacmedia.dsmz.de/medium/92Name: 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
18625ISP 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
18625ISP 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:
18625ISP 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
18625ISP 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
18625ISP 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
18625ISP 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
37734MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8555TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://bacmedia.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8555positivegrowth28mesophilic
37734positivegrowth25mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

compound production

@refcompound
8555steroids, 7-cyano
8555pregnadienes
85555' nucleotides
8555dienes
8555steroids, 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

@refsample type
8555soil
47831Rice soil
67770Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186251Hazard group
85551Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardioides simplex 16S ribosomal RNA gene, partial sequenceAF0050131474ena2045
20218Nocardioides simplex strain ATCC 15799 16S-23S internal transcribed spacer, complete sequenceAF017499386ena2045
20218N.simplex 16S rRNA geneZ782121468ena2045
20218Pimelobacter simplex strain KCTC 9106 16S ribosomal RNA gene, partial sequenceAF0050091474ena2045
20218Nocardioides simplex strain KCTC 9106 16S-23S internal transcribed spacer, complete sequenceAF017494386ena2045
20218Nocardioides simplex partial 16S rRNAX532131392ena2045
67770Arthobacter simplex small subunit ribosomal RNAM376931517ena2045

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pimelobacter simplex ATCC 6946GCA_900114845scaffoldncbi2045
66792Pimelobacter simplex NBRC 12069GCA_006538965contigncbi2045
66792Pimelobacter simplex strain ATCC 69462045.9wgspatric2045
66792Pimelobacter simplex strain NBRC 120692045.10wgspatric2045
66792Pimelobacter simplex ATCC 69462687453782draftimg2045
67770Pimelobacter simplex strain NBRC 12069, whole genome shotgun sequencing projectBJMC00000000ncbi2045
67770Pimelobacter simplex strain ATCC 6946, whole genome shotgun sequencing projectFOUK00000000ncbi2045

GC content

@refGC-contentmethod
855571.7
6777071.7thermal denaturation, midpoint method (Tm)
6777073thermal denaturation, midpoint method (Tm)
6777074
6777074.4thermal denaturation, midpoint method (Tm)
6777072.9genome sequence analysis

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

@refpassport
20218http://www.straininfo.net/strains/40113
20218http://www.straininfo.net/strains/40111
20218http://www.straininfo.net/strains/164005
20218http://www.straininfo.net/strains/98691
20218http://www.straininfo.net/strains/40115
20218http://www.straininfo.net/strains/122160
20218http://www.straininfo.net/strains/40117

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism1366455The use of free and immobilised Arthrobacter simplex in organic solvent/aqueous two-liquid-phase reactors.Hocknull MD, Lilly MDAppl Microbiol Biotechnol10.1007/BF001765161990Arthrobacter/*metabolism, Hydrocortisone/*metabolism, Kinetics, SolventsEnzymology
Metabolism1367800Delta'-dehydrogenation of steroids by Arthrobacter simplex immobilized in calcium polygalacturonate beads.Montes MC, Magana IJ Ind Microbiol10.1007/BF015760641991Arthrobacter/enzymology/*metabolism, Cortodoxone/*metabolism, Hydrocortisone/*metabolism, Hydrogen-Ion Concentration, Hydroxysteroid Dehydrogenases/*metabolism, Microspheres, Oxygen/metabolism, Pectins, Prednisolone/analysis/metabolism, Vitamin K/metabolismEnzymology
Enzymology8586617Purification and characterization of the 3-ketosteroid-delta 1-dehydrogenase of Arthrobacter simplex produced in Streptomyces lividans.Choi KP, Molnar I, Yamashita M, Murooka YJ Biochem10.1093/oxfordjournals.jbchem.a1248041995Amino 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, TemperatureGenetics
Phylogeny8757942Mineralization 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 NRJ Ind Microbiol10.1007/BF015700411996Base Sequence, Biodegradation, Environmental, Fatty Acids/analysis, Gram-Positive Bacteria/genetics/isolation & purification/*metabolism, Industrial Waste, Molecular Sequence Data, Phylogeny, Picrates/*metabolism, Species SpecificityMetabolism
Enzymology10930735Purification and characterization of histamine dehydrogenase from Nocardioides simplex IFO 12069.Siddiqui JA, Shoeb SM, Takayama S, Shimizu E, Yorifuji TFEMS Microbiol Lett10.1111/j.1574-6968.2000.tb09227.x2000Amine Oxidase (Copper-Containing)/*isolation & purification/*metabolism, Catalysis, Nocardiaceae/*enzymology, Substrate SpecificityPhylogeny
Metabolism11867272Conversion 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 TJ Steroid Biochem Mol Biol10.1016/s0960-0760(01)00176-52002Androstenedione/*metabolism, Arthrobacter/*metabolism, Liposomes/*chemistry/metabolism, Pectins/*metabolism, Solutions/chemistry, Water/chemistry/metabolism
Metabolism17936614Enhancement of androstadienedione production from progesterone by biotransformation using the hydroxypropyl-beta-cyclodextrin complexation technique.Manosroi A, Saowakhon S, Manosroi JJ Steroid Biochem Mol Biol10.1016/j.jsbmb.2007.05.03220072-Hydroxypropyl-beta-cyclodextrin, Androstenedione/*analogs & derivatives/*metabolism, Bacillus/metabolism, Bacteriological Techniques, Biotransformation/drug effects, Excipients/pharmacology, Progesterone/*pharmacokinetics, beta-Cyclodextrins/*pharmacologyBiotechnology
18597329Ultrasound-enhanced bioprocess. II: Dehydrogenation of hydrocortisone by Arthrobacter simplex.Zabaneh M, Bar RBiotechnol Bioeng10.1002/bit.2603711031991
Phylogeny19625430Nocardioides 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 DCInt J Syst Evol Microbiol10.1099/ijs.0.008821-02009Actinomycetales/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/*metabolismMetabolism
Phylogeny19628618Nocardioides caeni sp. nov., isolated from wastewater.Yoon JH, Kang SJ, Park S, Kim W, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.010124-02009Actinomycetales/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 MicrobiologyMetabolism
Metabolism23973392Increased 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 GSteroids10.1016/j.steroids.2013.07.00920132-Hydroxypropyl-beta-cyclodextrin, Androstadienes/*chemistry/*metabolism, Antineoplastic Agents/*chemistry/*metabolism, Arthrobacter/metabolism, Biotransformation, Solubility, Water/chemistry, beta-Cyclodextrins/*chemistryBiotechnology
Phylogeny24846051Nocardioides soli sp. nov., a bacterium isolated from a mountain soil.Srinivasan S, Lee SS, Lee JJ, Kim MKAntonie Van Leeuwenhoek10.1007/s10482-014-0191-72014Actinobacteria/*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/analysisPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8555Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20130)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20130
18625Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20130.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
37734Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11383
47831Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23611)https://www.ccug.se/strain?id=23611
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/