Strain identifier

BacDive ID: 16544

Type strain: Yes

Species: Nonomuraea rubra

Strain history: CIP <- 2001, JCM <- KCC <- VKM <- LIA 0743

NCBI tax ID(s): 46180 (species)

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General

@ref: 11056

BacDive-ID: 16544

DSM-Number: 43768

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic

description: Nonomuraea rubra DSM 43768 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 46180
  • Matching level: species

strain history

@refhistory
11056<- N.S. Agre, VKM (Micromonospora rubra)
67770DSM 43768 <-- VKM Ac-615 <-- LIA 0743.
122285CIP <- 2001, JCM <- KCC <- VKM <- LIA 0743

doi: 10.13145/bacdive16544.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiaceae
  • genus: Nonomuraea
  • species: Nonomuraea rubra
  • full scientific name: Nonomuraea rubra corrig. (Sveshnikova et al. 1969) Zhang et al. 1998

  • synonyms

    @refsynonym
    20215Micromonospora rubra
    20215Nonomuria rubra
    20215Actinomadura rubra
    20215Microtetraspora rubra

@ref: 11056

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Nonomuraea

species: Nonomuraea rubra

full scientific name: Nonomuraea rubra (Sveshnikova et al. 1969) Zhang et al. 1998

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.875
69480100positive
122285nofilament-shaped

colony morphology

@refcolony colorincubation periodmedium used
19953Purple red (3004)10-14 daysISP 2
19953Flame red (3000)10-14 daysISP 3
19953Orange red10-14 daysISP 4
19953Orange red10-14 daysISP 5
19953Tomato red (3013)10-14 daysISP 6
19953Tomato red (3013)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19953yesAerial MyceliumWhiteISP 2
19953yesAerial MyceliumWhiteISP 3
19953yesAerial MyceliumWhiteISP 4
19953yesAerial MyceliumSparse/ whiteISP 5
19953noISP 6
19953yesAerial MyceliumSparse/ whiteISP 7

multimedia

  • @ref: 11056
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43768.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11056ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
19953ISP 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
19953ISP 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:
19953ISP 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
19953ISP 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
19953ISP 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
19953ISP 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
37280MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
11056GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 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
122285CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19953positiveoptimum30mesophilic
37280positivegrowth30mesophilic
11056positivegrowth28mesophilic
67770positivegrowth28mesophilic
122285positivegrowth15-41
122285nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122285
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 19953
  • compound: Maduramycin

halophily

@refsaltgrowthtested relationconcentration
19953NaClpositivemaximum2.5 %
122285NaClpositivegrowth0-2 %
122285NaClnogrowth4 %
122285NaClnogrowth6 %
122285NaClnogrowth8 %
122285NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H6), MK-9(H4), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1995362968cellulose+
1995316634raffinose+
1995326546rhamnose+
1995328757fructose+
1995329864mannitol+
1995317268myo-inositol+
1995318222xylose+
1995317992sucrose+
1995322599arabinose+
1995317234glucose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1222854853esculin+hydrolysis
12228517234glucose+/-degradation
12228517632nitrate-respiration

antibiotic resistance

  • @ref: 122285
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12228535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12228515688acetoin-
12228517234glucose-

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
122285oxidase-
122285alcohol dehydrogenase-1.1.1.1
122285gelatinase+
122285amylase-
122285DNase+
122285caseinase+3.4.21.50
122285catalase+1.11.1.6
122285tween esterase+
122285gamma-glutamyltransferase+2.3.2.2
122285lecithinase-
122285lipase+
122285lysine decarboxylase-4.1.1.18
122285ornithine decarboxylase-4.1.1.17
122285phenylalanine ammonia-lyase-4.3.1.24
122285protease+
122285tryptophan deaminase-
122285urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382beta-galactosidase+3.2.1.23
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
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- FucosidaseControl
19953+-+-++-++++-++++---
122285+++-+--+-++++-++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19953+++++-+--++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122285---+/--+/-------------------+/--+/-+/--------+/-+/-------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122285+-+-+-+++++++++++-+-++----------------------------------------------------------------+--++------+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11056soil
67770SoilRussiaRUS
122285Environment, SoilRussian FederationRUSEurope

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
110561Risk group (German classification)
199531German classification
1222851Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microtetraspora rubra strain ATCC27031 16S ribosomal RNA gene, partial sequenceAF051393196ena46180
20218Nonomuraea rubra 16S ribosomal RNA gene, partial sequenceAF2772001457ena46180

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nonomuraea rubra DSM 43768GCA_014207985contigncbi46180
66792Nonomuraea rubra strain DSM 4376846180.3wgspatric46180
66792Nonomuraea rubra DSM 437682870609773draftimg46180

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes85.945no
anaerobicno98.645no
halophileno90.433no
spore-formingyes94.75no
glucose-utilyes87.365yes
aerobicyes89.98no
flagellatedno97.627no
thermophileno98.627no
motileno90.732no
glucose-fermentno92.739no

External links

@ref: 11056

culture collection no.: DSM 43768, ATCC 27031, CBS 132.76, DSM 43897, IFO 14070, IMET 8181, JCM 3234, KCC A-0234, NBRC 14070, VKM Ac-615, JCM 3389, BCRC 12591, CGMCC 4.5715, CIP 107008, IFO 14686, IMSNU 20099, INA 325, KCTC 9284, NBRC 14686, NRRL B-16083

straininfo link

  • @ref: 85574
  • straininfo: 389277

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22389281Nonomuraea jabiensis sp. nov., isolated from arid soil.Camas M, Sazak A, Sproer C, Klenk HP, Cetin D, Guven K, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.039362-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nigeria, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny32853131Nonomuraea antri sp. nov., an actinomycete isolated from cave soil in Thailand.Lipun K, Teo WFA, Suksaard P, Pathom-Aree W, Duangmal KInt J Syst Evol Microbiol10.1099/ijsem.0.0044132020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11056Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43768)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43768
19953Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43768.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
37280Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19202
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
85574Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389277.1StrainInfo: A central database for resolving microbial strain identifiers
122285Curators of the CIPCollection of Institut Pasteur (CIP 107008)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107008