Strain identifier

BacDive ID: 7839

Type strain: Yes

Species: Actinoplanes liguriensis

Strain Designation: A/6353, FH 2244

Strain history: <- BCRC <- IFO <- RICI <- KCC <- SANK <- ATCC <- Lepetit A/6353

NCBI tax ID(s): 69484 (species)

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General

@ref: 11346

BacDive-ID: 7839

DSM-Number: 43865

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive, antibiotic compound production

description: Actinoplanes liguriensis A/6353 is an aerobe, spore-forming, Gram-positive bacterium that produces antibiotic compounds and was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 69484
  • Matching level: species

strain history

@refhistory
11346<- ATCC <- Lepetit Labs., A/6353
67770KCC A-0250 <-- SANK 62178 <-- ATCC 31048 <-- Lepetit A/6353.
67771<- BCRC <- IFO <- RICI <- KCC <- SANK <- ATCC <- Lepetit A/6353

doi: 10.13145/bacdive7839.20240916.9.1

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 liguriensis
  • full scientific name: Actinoplanes liguriensis Wink et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Actinoplanes liguriae

@ref: 11346

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes liguriensis

full scientific name: Actinoplanes liguriensis Wink et al. 2006

strain designation: A/6353, FH 2244

type strain: yes

Morphology

cell morphology

  • @ref: 67771
  • gram stain: positive

colony morphology

@refcolony colorincubation periodmedium used
19609Yellow orange10-14 daysISP 2
19609Yellow orange10-14 daysISP 3
19609Yellow orange10-14 daysISP 4
19609Yellow orange10-14 daysISP 5
19609Yellow orange10-14 daysISP 6
19609Yellow orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19609noISP 2
19609noISP 3
19609noISP 4
19609noISP 5
19609noISP 6
19609noISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
11346https://www.dsmz.de/microorganisms/photos/DSM_43865-1.jpg© Leibniz-Institut DSMZ
11346https://www.dsmz.de/microorganisms/photos/DSM_43865.jpg© Leibniz-Institut DSMZMedium 554 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11346N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
11346GYM 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
19609ISP 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
19609ISP 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:
19609ISP 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
19609ISP 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
19609ISP 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
19609ISP 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

culture temp

@refgrowthtypetemperature
11346positivegrowth28
19609positiveoptimum28
67770positivegrowth28
67771positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
19609Formation of sporangia, spore surface smoothsporeyes
69480yes91.021

compound production

  • @ref: 11346
  • compound: gardimycin

halophily

  • @ref: 19609
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-10(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1960917234glucose+
1960922599arabinose-
1960917992sucrose-
1960918222xylose-
1960917268myo-inositol-
1960929864mannitol-
1960928757fructose-
1960926546rhamnose+
1960916634raffinose-
1960962968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770gardimycinyes
68368acetoinyes15688
68368indoleno35581
68368hydrogen sulfideno16136

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
19609+++-+--+++++++++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19609+-----+--++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11346garden soilItalyITAEurope
67770Garden soilItalyITAEuropeLiguria
67771From garden soilItalyITAEuropeLiguria

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113461Risk group (German classification)
196091Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinoplanes liguriensis gene for 16S rRNA, partial sequenceAB0474971475nuccore69484
20218Actinoplanes liguriensis partial 16S rRNA gene, strain IMSNU 22127AJ2775791488nuccore69484
11346Actinoplanes liguriensis 16S rRNA gene, type strain DSM 43865TAJ8654711438nuccore69484

Genome sequences

  • @ref: 67770
  • description: Actinoplanes liguriensis NRRL B-16723
  • accession: GCA_000715855
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 69484

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes86.718no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.833yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.407yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes91.021yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.75yes
69480flagellatedmotile2+Ability to perform flagellated movementno63.167no

External links

@ref: 11346

culture collection no.: DSM 43865, ATCC 31048, BCRC 12121, CBS 355.75, IFO 13997, IMSNU 22127, JCM 3250, KCC A-0250, KCTC 9536, NBRC 13997, NCIMB 12636, NRRL B-16723, SANK 62178, CGMCC 4.5521

straininfo link

  • @ref: 77276
  • straininfo: 389381

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957109Actinoplanes liguriensis sp. nov. and Actinoplanes teichomyceticus sp. nov.Wink JM, Kroppenstedt RM, Schumann P, Seibert G, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64240-02006Bacterial Typing Techniques, DNA, Bacterial/analysis, Micromonosporaceae/*classification/genetics/metabolism, Molecular Sequence Data, RNA, Ribosomal, 16S/*analysis/geneticsGenetics
Phylogeny23396720Actinoplanes siamensis sp. nov., isolated from soil.Suriyachadkun C, Ngaemthao W, Chunhametha S, Thawai C, Sanglier JJInt J Syst Evol Microbiol10.1099/ijs.0.048017-02013Bacterial Typing Techniques, Bambusa/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11346Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43865)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43865
19609Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43865.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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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)
77276Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389381.1StrainInfo: A central database for resolving microbial strain identifiers