Strain identifier

BacDive ID: 16549

Type strain: Yes

Species: Nonomuraea polychroma

Strain history: CIP <- 2002, JCM <- IFO <- INA

NCBI tax ID(s): 46176 (species)

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General

@ref: 11274

BacDive-ID: 16549

DSM-Number: 43925

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive

description: Nonomuraea polychroma DSM 43925 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 46176
  • Matching level: species

strain history

@refhistory
11274<- IMET <- T.P. Preobrazhenskaya, INA
67770IFO 14345 <-- INA 2755.
121926CIP <- 2002, JCM <- IFO <- INA

doi: 10.13145/bacdive16549.20230509.8.1

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 polychroma
  • full scientific name: Nonomuraea polychroma corrig. (Galatenko et al. 1987) Zhang et al. 1998

  • synonyms

    @refsynonym
    20215Nonomuria polychroma
    20215Actinomadura polychroma
    20215Microtetraspora polychroma

@ref: 11274

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Nonomuraea

species: Nonomuraea polychroma

full scientific name: Nonomuraea polychroma (Galatenko et al. 1987) Zhang et al. 1998

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
121926positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19982Ochre yellow (1024)10-14 daysISP 2
19982Opal green (6026)10-14 daysISP 3
19982Opal green (6026)10-14 daysISP 4
19982Opal green (6026)10-14 daysISP 5
19982Ochre yellow (1024)10-14 daysISP 6
19982Opal green (6026)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19982noISP 2
19982noISP 3
19982noISP 4
19982noISP 5
19982noISP 6
19982noISP 7

multimedia

  • @ref: 11274
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43925.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11274GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
11274GYM 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
19982ISP 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
19982ISP 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:
19982ISP 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
19982ISP 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
19982ISP 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
19982ISP 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
38203MEDIUM 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)
121926CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11274positivegrowth28mesophilic
19982positiveoptimum28mesophilic
38203positivegrowth30mesophilic
67770positivegrowth28mesophilic
121926positivegrowth30-41
121926nogrowth5psychrophilic
121926nogrowth15psychrophilic
121926nogrowth22psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
19982NaClpositivemaximum2.5 %
121926NaClnogrowth0 %
121926NaClnogrowth2 %
121926NaClnogrowth4 %
121926NaClnogrowth6 %
121926NaClnogrowth8 %
121926NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1998217234glucose+
1998222599arabinose-
1998217992sucrose-
1998218222xylose-
1998217268myo-inositol-
1998229864mannitol-
1998228757fructose-
1998226546rhamnose-
1998216634raffinose-
1998262968cellulose-
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
6837128087glycogen-builds acid from
6837128017starch-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
6837117306maltose-builds acid from
6837117057cellobiose-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
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-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
1219264853esculin+hydrolysis
12192617632nitrate+reduction
12192616301nitrite-reduction

antibiotic resistance

  • @ref: 121926
  • 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
12192635581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12192615688acetoin-
12192617234glucose-

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
121926oxidase-
121926alcohol dehydrogenase-1.1.1.1
121926gelatinase+
121926amylase-
121926DNase-
121926caseinase+3.4.21.50
121926catalase+1.11.1.6
121926tween esterase-
121926gamma-glutamyltransferase+2.3.2.2
121926lecithinase-
121926lipase+
121926lysine decarboxylase-4.1.1.18
121926ornithine decarboxylase-4.1.1.17
121926phenylalanine ammonia-lyase-4.3.1.24
121926tryptophan deaminase-
121926urease-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+
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
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

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19982+++-++++-++++++++++
121926+++-++-+-+-++-++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19982-+++-----++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121926------------------------+/-------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121926--------------------------------------------------------------+--+---------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11274soilTurkmenistanTKMAsia
67770SoilTurkmenistanTKMAsia
121926Environment, SoilTurkmenistanTKMAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112741Risk group (German classification)
199821German classification
1219261Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microtetraspora polychroma 16S rRNA geneU489771413ena46176
67770Nonomuraea polychroma gene for 16S ribosomal RNA, partial sequence, strain: JCM 6834LC1115291426ena46176

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nonomuraea polychroma strain DSM 4392546176.3wgspatric46176
66792Nonomuraea polychroma DSM 439252808606959draftimg46176
67770Nonomuraea polychroma DSM 43925GCA_004011505contigncbi46176

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes87.018no
anaerobicno98.67no
halophileno90.482no
spore-formingyes93.318no
glucose-utilyes89.324yes
aerobicyes89.907no
flagellatedno97.603no
thermophileno98.294no
motileno90.669no
glucose-fermentno91.542no

External links

@ref: 11274

culture collection no.: DSM 43925, IFO 14345, IMET 9743, INA 2755, NBRC 14345, NRRL B-16243, VKM Ac-1084, JCM 6834, ATCC 49500, BCRC 16335, CIP 107354, IMSNU 20094, KCTC 9277

straininfo link

  • @ref: 85579
  • straininfo: 42517

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny6459758[New species of Actinomadura isolated from soils in Turkmenia and their antagonistic properties].Galatenko OA, Terekhova LP, Preobrazhenskaia TPAntibiotiki1981Actinomycetales/*classification/cytology/isolation & purification, *Antibiosis, *Soil Microbiology, TurkmenistanEnzymology
Phylogeny32519020Nonomuraea terrae sp. nov., isolated from arid soil.Ay HArch Microbiol2020Actinobacteria/classification/genetics, Actinomycetales/chemistry/*classification/genetics/isolation & purification, Base Composition, Fatty Acids/analysis, Genome, Bacterial/genetics, Phospholipids/analysis, Phylogeny, Soil/chemistry, *Soil Microbiology, TurkeyGenetics10.1007/s00203-020-01941-9
Phylogeny32790600Nonomuraea nitratireducens sp. nov., a new actinobacterium isolated from Suaeda australis Moq. rhizosphere.Ou Y, Sheng Y, Hu X, Leng D, Huang J, Hu Z, Bai L, Deng Z, Kang Q, Wu YInt J Syst Evol Microbiol2020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome10.1099/ijsem.0.004377

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11274Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43925)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43925
19982Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43925.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
38203Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4780
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/
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
85579Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42517.1StrainInfo: A central database for resolving microbial strain identifiers
121926Curators of the CIPCollection of Institut Pasteur (CIP 107354)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107354