Strain identifier

BacDive ID: 16546

Type strain: Yes

Species: Nonomuraea spiralis

Strain Designation: 832-34

Strain history: CIP <- 2001, CCM <- IMET, Actinomadura spiralis

NCBI tax ID(s): 46182 (species)

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General

@ref: 11142

BacDive-ID: 16546

DSM-Number: 43555

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

description: Nonomuraea spiralis 832-34 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 46182
  • Matching level: species

strain history

@refhistory
11142<- IMET <- J. Meyer, 832-34
67770KCC A-0286 <-- IMET 9621 <-- J. Meyer 832-34.
123263CIP <- 2001, CCM <- IMET, Actinomadura spiralis

doi: 10.13145/bacdive16546.20230509.8.1

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 spiralis
  • full scientific name: Nonomuraea spiralis corrig. (Meyer 1981) Zhang et al. 1998

  • synonyms

    @refsynonym
    20215Actinomadura spiralis
    20215Nonomuria spiralis
    20215Microtetraspora spiralis

@ref: 11142

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Nonomuraea

species: Nonomuraea spiralis

full scientific name: Nonomuraea spiralis (Meyer 1981) Zhang et al. 1998

strain designation: 832-34

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.851
69480100positive
123263nopositivefilament-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33019MEDIUM 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)
11142GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yesName: 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 waterhttps://mediadive.dsmz.de/medium/65
123263CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
18495positiveoptimum30mesophilic
33019positivegrowth30mesophilic
11142positivegrowth28mesophilic
67770positivegrowth28mesophilic
123263positivegrowth22-37
123263nogrowth5psychrophilic
123263nogrowth15psychrophilic
123263nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123263
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
18495NaClpositivemaximum2.5 %
123263NaClpositivegrowth0 %
123263NaClnogrowth2 %
123263NaClnogrowth4 %
123263NaClnogrowth6 %
123263NaClnogrowth8 %
123263NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1849517234glucose+
1849522599arabinose-
1849517992sucrose+
1849518222xylose+
1849517268myo-inositol-
1849529864mannitol+
1849528757fructose-
1849526546rhamnose+
1849516634raffinose-
1849562968cellulose-
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
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
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-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
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
6837117113erythritol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
1232634853esculin-hydrolysis
12326317632nitrate+reduction
12326316301nitrite-reduction
12326317632nitrate-respiration

antibiotic resistance

  • @ref: 123263
  • 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
12326335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12326315688acetoin-
12326317234glucose-

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
123263oxidase-
123263beta-galactosidase+3.2.1.23
123263alcohol dehydrogenase-1.1.1.1
123263gelatinase+/-
123263amylase-
123263DNase-
123263caseinase-3.4.21.50
123263catalase+1.11.1.6
123263gamma-glutamyltransferase+2.3.2.2
123263lysine decarboxylase-4.1.1.18
123263ornithine decarboxylase-4.1.1.17
123263phenylalanine ammonia-lyase-4.3.1.24
123263tryptophan deaminase-
123263urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382acid phosphatase+3.1.3.2
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

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18495+-+-++-+++-++-+++++
123263++--+----++-+-+++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18495+--------+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123263+/--+/-+/-+/-------+/------+/----+/---+/-+/-+/-+/----+/-----------+/-+/------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123263+++++----++-+-----++++-++------+-+---+-----------+---------+--+---+---++++++---++-------+++-------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11142soilTokyo, Ueno ParkJapanJPNAsia
67770SoilUeno Park, TokyoJapanJPNAsia
123263Environment, SoilTokyoJapanJPNAsia1969

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
111421Risk group (German classification)
184951German classification
1232631Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11142
  • description: Microtetraspora spiralis 16S rRNA gene
  • accession: U48983
  • length: 1409
  • database: ena
  • NCBI tax ID: 46182

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nonomuraea spiralis JCM 3286GCA_014648435scaffoldncbi46182
66792Nonomuraea spiralis strain JCM 328646182.4wgspatric46182

GC content

  • @ref: 67770
  • GC-content: 68.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.062no
gram-positiveyes86.516no
anaerobicno99.027no
aerobicyes93.304no
halophileno93.453no
spore-formingyes95.476no
thermophileno98.444yes
glucose-utilyes89.822yes
motileno92.181no
glucose-fermentno93.063no

External links

@ref: 11142

culture collection no.: DSM 43555, ATCC 35114, CCM 3426, IFO 14097, IMET 9621, JCM 3286, KCC A-0286, NBRC 14097, NCIB 11633, NRRL B-16098, BCRC 13309, CIP 106923, IMSNU 20101, KCTC 9286, NCIMB 11633, VKM Ac-853, CCRC 13309

straininfo link

  • @ref: 85576
  • straininfo: 50759

Reference

@idauthorscataloguedoi/urltitle
11142Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43555)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43555
18495Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43555.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
33019Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19107
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
85576Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50759.1StrainInfo: A central database for resolving microbial strain identifiers
123263Curators of the CIPCollection of Institut Pasteur (CIP 106923)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106923