Strain identifier

BacDive ID: 8036

Type strain: Yes

Species: Virgisporangium aurantiacum

Strain Designation: Yu 438-5

Strain history: CIP <- 2003 JCM <- 2001, IFO <- T. Tamura: strain YU 438-5 <- M. Hayakawa: strain YU 438-5

NCBI tax ID(s): 175570 (species)

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General

@ref: 11981

BacDive-ID: 8036

DSM-Number: 44794

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

description: Virgisporangium aurantiacum Yu 438-5 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil vegetable field.

NCBI tax id

  • NCBI tax id: 175570
  • Matching level: species

strain history

@refhistory
11981<- NBRC <- IFO <- M. Hayakawa, Yamanashi Univ.; Yu 438-5
67770T. Tamura YU 438-5 <-- M. Hayakawa YU 438-5.
67771<- IFO
116559CIP <- 2003 JCM <- 2001, IFO <- T. Tamura: strain YU 438-5 <- M. Hayakawa: strain YU 438-5

doi: 10.13145/bacdive8036.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Virgisporangium
  • species: Virgisporangium aurantiacum
  • full scientific name: Virgisporangium aurantiacum corrig. Tamura et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Virgosporangium aurantiacum

@ref: 11981

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Virgisporangium

species: Virgisporangium aurantiacum

full scientific name: Virgisporangium aurantiacum Tamura et al. 2001

strain designation: Yu 438-5

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
67771positive
69480positive100
116559positivefilament-shapedno

colony morphology

@refcolony colormedium used
69363Deep orange (2011)ISP 6
69363Clay brown (8003)ISP 7
69363Bright red orange (2008)ISP 3
69363Bright red orange (2008)ISP 4
69363Bright red orange (2008)ISP 5
69363Bright red orange (2008)ISP 2
69363Yellow orange (2000)suter without tyrosine
69363Yellow orange (2000), clay brown (8003)suter with tyrosine
116559

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69363noAerial myceliumISP 2
69363noAerial myceliumISP 3
69363noAerial myceliumISP 4
69363noAerial myceliumISP 5
69363noAerial myceliumISP 6
69363noAerial myceliumISP 7
69363noAerial myceliumsuter with tyrosine
69363noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
69363yesMelanin
69363yessoluble pigmentClay brown (8003)

multimedia

@refmultimedia contentcaptionintellectual property rights
11981https://www.dsmz.de/microorganisms/photos/DSM_44794.jpgMedium 65 28°C© Leibniz-Institut DSMZ
69363DSM_44794_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69363DSM_44794_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11981ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
38193MEDIUM 366 - for Actinoalloteichus cyanogriseusyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
11981GYM 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
116559CIP Medium 366yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=366

culture temp

@refgrowthtypetemperaturerange
11981positivegrowth28mesophilic
38193positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic
116559positivegrowth10-30
116559nogrowth37mesophilic
116559nogrowth41thermophilic
116559nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
116559obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
69363NaClpositivegrowth0 %
116559NaClpositivegrowth0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H8), MK-10(H4), MK-10(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6936322599arabinose+growth
6936362968cellulose+/-growth
6936328757fructose+growth
6936317234glucose+growth
6936317268inositol+/-growth
6936337684mannose+growth
6936316634raffinose+growth
6936326546rhamnose+growth
6936317992sucrose+growth
6936318222xylose+growth
11655916947citrate-carbon source
1165594853esculin+hydrolysis
116559606565hippurate-hydrolysis
11655917632nitrate-reduction
11655916301nitrite-reduction
11655917632nitrate-respiration
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 116559
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116559
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11655915688acetoin-
11655917234glucose-

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
116559oxidase-
116559beta-galactosidase+3.2.1.23
116559gelatinase+
116559amylase+
116559DNase+
116559caseinase+3.4.21.50
116559catalase+1.11.1.6
116559tween esterase+
116559gamma-glutamyltransferase+2.3.2.2
116559lecithinase-
116559lipase-
116559phenylalanine ammonia-lyase-4.3.1.24
116559protease+
116559tryptophan deaminase-
116559urease-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+
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-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69363+-++-++-+-++/--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
69363+++-+++/-++++++-++++-
116559+++-++---++++-+++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11981soil vegetable fieldJapanJPNAsia
67770Soil of vegetable fieldJapanJPNAsiaYamanashi Pref.
67771From soilJapanJPNAsia
116559Environment, Soil, vegetable fieldJapanJPNAsiaYamanashi

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119811Risk group (German classification)
201201German classification
1165591Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11981
  • description: Virgosporangium aurantiacum gene for 16S rRNA, partial sequence, strain:YU438-5
  • accession: AB006169
  • length: 1469
  • database: ena
  • NCBI tax ID: 175570

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Virgisporangium aurantiacum NBRC 16421GCA_016863635contigncbi175570
66792Virgisporangium aurantiacum strain NBRC 16421175570.3wgspatric175570

GC content

@refGC-contentmethod
1198171
6777071high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes64.453no
gram-positiveyes84.346yes
anaerobicno99.061yes
aerobicyes90.572yes
halophileno94.786no
spore-formingyes85.49no
thermophileno99.31no
glucose-utilyes87.726no
flagellatedno91.401no
glucose-fermentno89.557no

External links

@ref: 11981

culture collection no.: DSM 44794, CCUG 46559, CIP 107212, IFO 16421, JCM 11002, KCTC 13916, NBRC 16421, BCRC 16331, CGMCC 4.5555

straininfo link

  • @ref: 77466
  • straininfo: 101058

Reference

@idauthorscataloguedoi/urltitle
11981Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44794)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44794
20120Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44794.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
38193Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4623
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69363Wink, J.https://cdn.dsmz.de/wink/DSM%2044794.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
77466Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID101058.1StrainInfo: A central database for resolving microbial strain identifiers
116559Curators of the CIPCollection of Institut Pasteur (CIP 107212)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107212