Strain identifier

BacDive ID: 11099

Type strain: Yes

Species: Nocardioides jensenii

Strain history: CIP <- 1986, DSM, Pimelobacter jensenii <- NCIB <- C.W. Evans <- H.L. Jensen, Corynebacterium simplex

NCBI tax ID(s): 1303683 (strain), 1843 (species)

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General

@ref: 8987

BacDive-ID: 11099

DSM-Number: 20641

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Nocardioides jensenii DSM 20641 is a mesophilic bacterium that was isolated from Soil.

NCBI tax id

NCBI tax idMatching level
1843species
1303683strain

strain history

@refhistory
8987<- NCIB <- C.W. Evans <- H.L. Jensen (Corynebacterium simplex)
67770K. Suzuki CNF 091 <-- IAM 12581 <-- NCIB 9770 <-- C. W. Evans <-- H. L. Jensen.
120342CIP <- 1986, DSM, Pimelobacter jensenii <- NCIB <- C.W. Evans <- H.L. Jensen, Corynebacterium simplex

doi: 10.13145/bacdive11099.20230509.8.1

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 jensenii
  • full scientific name: Nocardioides jensenii (Suzuki and Komagata 1983) Collins et al. 1989

  • synonyms

    • @ref: 20215
    • synonym: Pimelobacter jensenii

@ref: 8987

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides jensenii

full scientific name: Nocardioides jensenii (Suzuki and Komagata 1983) Collins et al. 1989

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
18452Transparent10-14 daysISP 2
18452Transparent10-14 daysISP 3
18452Transparent10-14 daysISP 4
18452Transparent10-14 daysISP 5
18452Transparent10-14 daysISP 6
18452Transparent10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18452noISP 2
18452noISP 3
18452noISP 4
18452noISP 5
18452noISP 6
18452noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8987TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.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
18452ISP 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
18452ISP 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:
18452ISP 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
18452ISP 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
18452ISP 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
18452ISP 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
39665MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120342CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
8987positivegrowth28mesophilic
39665positivegrowth25mesophilic
54002positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

halophily

  • @ref: 18452
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 8987
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

observation

@refobservation
20216Degrades dinitro-o-cresol herbicides
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    54002C14:00.414
    54002C15:01.315
    54002C16:04.116
    54002C17:03.517
    54002C18:0218
    54002C13:0 3OH/C15:1 i I/H0.314.469
    54002C13:0 iso0.212.612
    54002C14:0 ISO0.613.618
    54002C15:0 ANTEISO0.614.711
    54002C15:0 ISO8.614.621
    54002C15:0 ISO 3OH0.416.135
    54002C15:1 ω6c0.314.856
    54002C16:0 2OH0.517.233
    54002C16:0 iso13.915.626
    54002C16:1 ISO H2.715.461
    54002C16:1 ω7c3.115.819
    54002C16:1 ω9c0.315.774
    54002C17:0 10-methyl1.117.41
    54002C17:0 anteiso1.816.722
    54002C17:0 iso5.316.629
    54002C17:1 ω6c3.416.862
    54002C17:1 ω8c5.616.792
    54002C17:1 ω9c ISO1.816.416
    54002C18:0 ISO0.517.632
    54002C18:1 ω7c /12t/9t0.917.824
    54002C18:1 ω9c1517.769
    54002C19:0 ANTEISO0.418.729
    54002TBSA 10Me18:0218.392
    54002Unidentified1.414.929
    54002Unidentified815.938
    54002Unidentified1.216.296
    54002Unidentified1.116.938
    54002Unidentified1.617.115
    54002Unidentified1.417.304
    54002Unidentified1.117.879
    54002Unidentified318.098
    54002Unidentified0.518.31
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphatase
18452+--+++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18452----+-+--++

Isolation, sampling and environmental information

isolation

@refsample type
54002Soil
67770Soil
120342Environment, Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2445.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1270;97_1506;98_1833;99_2445&stattab=map
  • Last taxonomy: Nocardioides jensenii
  • 16S sequence: Z78210
  • Sequence Identity:
  • Total samples: 55
  • soil counts: 23
  • aquatic counts: 5
  • animal counts: 24
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
89871Risk group (German classification)
184521
1203421Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardioides jensenii partial 16S rRNAX532141452ena1843
20218N.jensenii 16S rRNA geneZ782101467ena1843
20218Nocardioides jensenii 16S ribosomal RNA gene, partial sequenceAF0050061473ena1843
20218Nocardioides jensenii strain KCTC 9134 16S-23S internal transcribed spacer, complete sequenceAF017491344ena1843

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides jensenii JCM 1364 = NBRC 14755GCA_001313485contigncbi1303683
66792Nocardioides jensenii JCM 1364 = NBRC 147551303683.6wgspatric1303683
66792Nocardioides jensenii JCM 1364 = NBRC 147551303683.4wgspatric1303683
66792Nocardioides jensenii JCM 1364, NBRC 147552731957589draftimg1303683
66792Nocardioides jensenii JCM 1364, NBRC 147552734481948draftimg1303683
67770Nocardioides jensenii JCM 1364 = NBRC 14755GCA_001552535contigncbi1303683

GC content

@refGC-contentmethod
898768.8
6777068.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.373no
gram-positiveyes89.661no
anaerobicno98.971no
halophileno90.974no
spore-formingno88.005no
thermophileno99.032yes
glucose-utilyes88.51no
aerobicyes96.422no
flagellatedno98.493no
glucose-fermentno93.888no

External links

@ref: 8987

culture collection no.: DSM 20641, ATCC 49810, IAM 12581, IFO 14755, IMET 10678, JCM 1364, NBRC 14755, NCIB 9770, CCUG 37988, CIP 102404, CNF 091, IMSNU 22036, KCTC 9134, LMG 16325, NCIMB 9770, PCM 2328, VKM Ac-1878

straininfo link

  • @ref: 80348
  • straininfo: 9324

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625163Marmoricola aequoreus sp. nov., a novel actinobacterium isolated from marine sediment.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.64696-02007Actinomycetales/chemistry/*classification/*isolation & purification/physiology, Aerobiosis, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Vitamin K 2/analysisGenetics
Phylogeny18363057Nocardioides dilutes sp. nov. isolated from soil in Bigeum Island, Korea.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJCurr Microbiol10.1007/s00284-008-9125-92008Actinomycetales/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis/metabolism, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny19667373Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil.Yoon JH, Park S, Kang SJ, Lee JS, Lee KC, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.015354-02009Actinomycetales/classification/*genetics/isolation & purification/physiology, DNA, Bacterial/genetics, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny19915109Nocardioides mesophilus sp. nov., isolated from soil.Dastager SG, Lee JC, Pandey A, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.019059-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Temperature, Vitamin K 2/analysisGenetics
Phylogeny20935090Nocardioides iriomotensis sp. nov., an actinobacterium isolated from forest soil.Yamamura H, Ohkubo SY, Nakagawa Y, Ishida Y, Hamada M, Otoguro M, Tamura T, Hayakawa MInt J Syst Evol Microbiol10.1099/ijs.0.025080-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Japan, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, TreesGenetics
Phylogeny21742819Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant.Woo SG, Srinivasan S, Yang J, Jung YA, Kim MK, Lee MInt J Syst Evol Microbiol10.1099/ijs.0.033308-02011Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Denitrification, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analysisGenetics
Phylogeny27170166Nocardioides pakistanensis sp. nov., isolated from a hot water spring of Tatta Pani in Pakistan.Amin A, Ahmed I, Habib N, Abbas S, Xiao M, Hozzein WN, Li WJAntonie Van Leeuwenhoek10.1007/s10482-016-0711-82016Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Aerobiosis, Bacterial Typing Techniques, Diaminopimelic Acid/analysis, Fatty Acids/metabolism, Hot Springs/*microbiology, Nucleic Acid Hybridization, Pakistan, Phenotype, Phospholipids/metabolism, Phylogeny, Sequence Analysis, DNA, Sodium Chloride/metabolism, Water MicrobiologyMetabolism
Phylogeny27411814Nocardioides gilvus sp. nov., isolated from Namtso Lake.Zhang HX, Wang K, Xu ZX, Chen GJ, Du ZJAntonie Van Leeuwenhoek10.1007/s10482-016-0735-02016Actinomycetales/classification/*isolation & purification, Base Composition, DNA, Bacterial, Lakes/*microbiology, Molecular Typing, PhylogenyEnzymology
Phylogeny31637662Nocardioides jejuensis sp. nov., isolated from soil.Jang JH, Maeng S, Jung HY, Kim MK, Subramani GAntonie Van Leeuwenhoek10.1007/s10482-019-01343-y2019DNA, Bacterial, Genome, Bacterial, Genomics/methods, Phylogeny, Propionibacterium/*classification/genetics/*isolation & purification, RNA, Ribosomal, 16S, *Soil Microbiology, Whole Genome SequencingGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8987Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20641)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20641
18452Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20641.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
39665Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14086
54002Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37988)https://www.ccug.se/strain?id=37988
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
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
80348Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9324.1StrainInfo: A central database for resolving microbial strain identifiers
120342Curators of the CIPCollection of Institut Pasteur (CIP 102404)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102404