Strain identifier

BacDive ID: 7812

Type strain: Yes

Species: Actinoplanes regularis

Strain Designation: UNCC 79

Strain history: KCC A-0062 <-- CBS 193.64 <-- J. N. Couch UNCC 79.

NCBI tax ID(s): 52697 (species)

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General

@ref: 10821

BacDive-ID: 7812

DSM-Number: 43151

keywords: genome sequence, 16S sequence, Bacteria, spore-forming

description: Actinoplanes regularis UNCC 79 is a spore-forming bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 52697
  • Matching level: species

strain history

@refhistory
10821<- KCC <- CBS <- J.N. Couch, UNCC, 79
67770KCC A-0062 <-- CBS 193.64 <-- J. N. Couch UNCC 79.

doi: 10.13145/bacdive7812.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Actinoplanes
  • species: Actinoplanes regularis
  • full scientific name: Actinoplanes regularis (Couch 1963) Stackebrandt and Kroppenstedt 1988

  • synonyms

    @refsynonym
    20215Ampullaria regularis
    20215Ampullariella regularis

@ref: 10821

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes regularis

full scientific name: Actinoplanes regularis (Couch 1963) Stackebrandt and Kroppenstedt 1988 emend. Nouioui et al. 2018

strain designation: UNCC 79

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19549Brown red10-14 daysISP 2
19549Light orange10-14 daysISP 3
19549Orange10-14 daysISP 4
19549Orange10-14 daysISP 5
19549Light orange10-14 daysISP 6
19549Light orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19549noISP 2
19549noISP 3
19549noISP 4
19549noISP 5
19549noISP 6
19549noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19549ISP 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
19549ISP 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:
19549ISP 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
19549ISP 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
19549ISP 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
19549ISP 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
10821CZAPEK PEPTONE AGAR (DSMZ Medium 83)yesName: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled waterhttps://mediadive.dsmz.de/medium/83
10821CZAPEK-DOX AGAR (DSMZ Medium 130)yesName: CZAPEK-DOX AGAR (DSMZ Medium 130) Composition: Sucrose 30.0 g/l Agar 13.0 g/l NaNO3 3.0 g/l K2HPO4 1.0 g/l KCl 0.5 g/l MgSO4 x 7 H2O 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled waterhttps://mediadive.dsmz.de/medium/130
10821GYM 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

culture temp

@refgrowthtypetemperature
19549positiveoptimum28
10821positivegrowth28
67770positivegrowth28

Physiology and metabolism

spore formation

@refspore descriptiontype of sporespore formationconfidence
19549Spore surface: smooth, sporangia: +sporeyes
69480yes90.163
69481yes99

halophily

  • @ref: 19549
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1954917234glucose+
1954922599arabinose+
1954917992sucrose+
1954918222xylose-
1954917268myo-inositol-
1954929864mannitol-
1954928757fructose+
1954926546rhamnose+
1954916634raffinose-
1954962968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

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
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
19549-++-----++----++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19549+++++-++-++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10821garden soil
67770SoilUniversity of Wisconsin, Madison, WIUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
108211Risk group (German classification)
195491Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218A.regularis 16S rRNA geneX931881440nuccore52697
20218Actinoplanes regularis gene for 16S rRNA, partial sequenceAB0370111471nuccore52697

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinoplanes regularis NBRC 12514GCA_016862355contigncbi52697
66792Actinoplanes regularis strain DSM 4315152697.3wgspatric52697
66792Actinoplanes regularis strain NBRC 1251452697.4wgspatric52697
66792Actinoplanes regularis DSM 431512724679777draftimg52697
67770Actinoplanes regularis DSM 43151GCA_900188005scaffoldncbi52697

GC content

  • @ref: 67770
  • GC-content: 70.3
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes99no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes87.346no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.337no
69480spore-formingspore-formingAbility to form endo- or exosporesyes90.163no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.664no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.25yes
69480flagellatedmotile2+Ability to perform flagellated movementno62.833no

External links

@ref: 10821

culture collection no.: DSM 43151, CBS 193.64, IAM 14279, IFO 12514, IMET 9268, JCM 3062, KCC A-0062, NBRC 12514, RIA 821, BCC 49176, HAMBI 1928, IFM 1241, KCTC 9119, NCIMB 12730, NRRL B-3347, TBRC 168, VKM Ac-650

straininfo link

  • @ref: 77254
  • straininfo: 265446

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10821Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43151)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43151
19549Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43151.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
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
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
77254Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265446.1StrainInfo: A central database for resolving microbial strain identifiers