Strain identifier

BacDive ID: 11108

Type strain: Yes

Species: Nocardioides plantarum

Strain Designation: J70

Strain history: CIP <- 1994, NCIMB <- M.D. Collins, UK <- J. Grainger: strain J70

NCBI tax ID(s): 29299 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4173

BacDive-ID: 11108

DSM-Number: 11054

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

description: Nocardioides plantarum J70 is a mesophilic bacterium that was isolated from herbage.

NCBI tax id

  • NCBI tax id: 29299
  • Matching level: species

strain history

@refhistory
4173<- H. Prauser <- M. D. Collins <- J. M. Grainger, J70
67770NCIMB 12834 <-- M. D. Collins <-- J. M. Grainger J70.
121865CIP <- 1994, NCIMB <- M.D. Collins, UK <- J. Grainger: strain J70

doi: 10.13145/bacdive11108.20230509.8.1

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 plantarum
  • full scientific name: Nocardioides plantarum Collins et al. 1994

@ref: 4173

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides plantarum

full scientific name: Nocardioides plantarum Collins et al. 1994

strain designation: J70

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.962
69480100positive
121865nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
18359Sand yellow (1002)10-14 daysISP 2
18359Light ivory (1015)10-14 daysISP 3
18359Light ivory (1015)10-14 daysISP 4
18359Light ivory (1015)10-14 daysISP 5
18359Ivory (1014)10-14 daysISP 6
18359Brown beige (1011)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18359noISP 2
18359noISP 3
18359noISP 4
18359noISP 5
18359noISP 6
18359noISP 7

multimedia

  • @ref: 4173
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_11054.jpg
  • caption: Medium 92 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4173TRYPTICASE 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
18359ISP 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
18359ISP 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
18359ISP 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
18359ISP 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
18359ISP 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
18359ISP 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:
34128MEDIUM 111 - for ClavibacteryesDistilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(15.000 g);Glucose (5.000 g);Yeast extract (5.000 g);Trypticase peptone (10.000 g)
4173TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.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
121865CIP Medium 111yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=111

culture temp

@refgrowthtypetemperaturerange
18359positiveoptimum28mesophilic
4173positivegrowth28mesophilic
34128positivegrowth22psychrophilic
67770positivegrowth28mesophilic
121865positivegrowth15-22psychrophilic
121865nogrowth10psychrophilic
121865nogrowth30mesophilic
121865nogrowth37mesophilic
121865nogrowth41thermophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.985

halophily

@refsaltgrowthtested relationconcentration
18359NaClpositivemaximum10 %
121865NaClpositivegrowth0-2 %
121865NaClnogrowth4 %
121865NaClnogrowth6 %
121865NaClnogrowth8 %
121865NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1835917234glucose+
1835922599arabinose+
1835917992sucrose+
1835918222xylose-
1835917268myo-inositol-
1835929864mannitol-
1835928757fructose+
1835926546rhamnose+
1835916634raffinose-
1835962968cellulose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
1218654853esculin-hydrolysis
12186517632nitrate-reduction
12186516301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12186535581indoleno

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
121865oxidase-
121865beta-galactosidase-3.2.1.23
121865alcohol dehydrogenase-1.1.1.1
121865gelatinase-
121865amylase-
121865DNase+
121865caseinase-3.4.21.50
121865catalase+1.11.1.6
121865lysine decarboxylase-4.1.1.18
121865ornithine decarboxylase-4.1.1.17
121865urease-3.5.1.5
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
18359++++++++-++---++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18359----+----+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121865-+-+---+-------++++----+-------+----------------++----------+------------------++-------+---+------

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
4173herbage
67770Herbage
121865Grassland1963

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_43178.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_7953;97_17569;98_21830;99_43178&stattab=map
  • Last taxonomy: Nocardioides plantarum
  • 16S sequence: Z78211
  • Sequence Identity:
  • Total samples: 957
  • soil counts: 192
  • aquatic counts: 237
  • animal counts: 444
  • plant counts: 84

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
41731Risk group (German classification)
183591
1218651Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardioides plantarum strain NCIMB 12834 16S ribosomal RNA gene, partial sequenceAF0050081490ena29299
20218Nocardioides plantarum strain NCIMB 12834 16S-23S internal transcribed spacer, complete sequenceAF017493438ena29299
20218N.plantarum 16S rRNA geneZ782111484ena29299
4173N.plantarum gene for 16S rRNAX699731512ena29299

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides plantarum strain DSM 1105429299.3wgspatric29299
67770Nocardioides plantarum DSM 11054GCA_006346395contigncbi29299

GC content

  • @ref: 4173
  • GC-content: 69
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno66no
gram-positiveyes92.654no
anaerobicno98.944no
halophileno94.227no
spore-formingno72.65no
glucose-utilyes87.627no
motileno97.178no
thermophileno99.368yes
flagellatedno98.94no
aerobicyes95.277no
glucose-fermentno92.414no

External links

@ref: 4173

culture collection no.: DSM 11054, NCIMB 12834, Grainger J70, JCM 9626, ATCC 51889, CIP 104157, IMSNU 22067, KCTC 9577, LMG 16210, VKM Ac-1998

straininfo link

  • @ref: 80357
  • straininfo: 9325

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7520740Phylogenetic analysis of a new LL-diaminopimelic acid-containing coryneform bacterium from herbage, Nocardioides plantarum sp. nov.Collins MD, Cockcroft S, Wallbanks SInt J Syst Bacteriol10.1099/00207713-44-3-5231994Actinomycetales/*classification/genetics/*metabolism, Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/*metabolism, Genes, Bacterial, Molecular Sequence Data, Phylogeny, Plants/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityMetabolism
Phylogeny21515700Nocardioides ginsengagri sp. nov., isolated from the soil of a ginseng field.Lee SH, Liu QM, Lee ST, Kim SC, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.031823-02011Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Panax/growth & development, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny23264497Nocardioides marinquilinus sp. nov., isolated from coastal seawater.Cho Y, Jang GI, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.047902-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny24696303Nocardioides rubroscoriae sp. nov., isolated from volcanic ash.Lee SD, Lee DWAntonie Van Leeuwenhoek10.1007/s10482-014-0161-02014Actinomycetales/*classification/genetics/*isolation & purification/physiology, 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, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Volcanic EruptionsGenetics
Phylogeny25951861Nocardioides antarcticus sp. nov., isolated from marine sediment.Deng S, Chang X, Zhang Y, Ren L, Jiang F, Qu Z, Peng FInt J Syst Evol Microbiol10.1099/ijs.0.0003092015Actinomycetales/*classification/genetics/isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny28777069Nocardioides litoris sp. nov., isolated from the Taean seashore.Lee DW, Lee AH, Lee H, Kim JJ, Khim JS, Yim UH, Kim BSInt J Syst Evol Microbiol10.1099/ijsem.0.0019542017Actinomycetales/*classification/genetics/isolation & purification, Ammotherapy, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32375979Nocardioides dongxiaopingii sp. nov., isolated from leaves of Lamiophlomis rotata on the Qinghai-Tibet Plateau.Zhang S, Wang X, Yang J, Lu S, Lai XH, Jin D, Huang Y, Zhu W, Li J, Pu J, Huang Y, Tian Z, Dong K, Zhang G, Lei W, Wang S, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0041612020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lamiaceae/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4173Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11054)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11054
18359Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM11054.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
34128Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16035
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
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)
80357Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9325.1StrainInfo: A central database for resolving microbial strain identifiers
121865Curators of the CIPCollection of Institut Pasteur (CIP 104157)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104157