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Strain identifier

BacDive ID: 16930

Type strain: Yes

Species: Actinomadura livida

Strain history: DSM 43677 <-- N. S. Agre.

NCBI tax ID(s): 79909 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11240

BacDive-ID: 16930

DSM-Number: 43677

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Actinomadura livida DSM 43677 is a mesophilic bacterium of the family Thermomonosporaceae.

NCBI tax id

  • NCBI tax id: 79909
  • Matching level: species

strain history

doi: 10.13145/bacdive16930.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinomadura
  • species: Actinomadura livida
  • full scientific name: Actinomadura livida Lavrova and Preobrazhenskaya 1975 (Approved Lists 1980)

@ref: 11240

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura livida

full scientific name: Actinomadura livida Lavrova and Preobrazhenskaya 1975

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 96.573

colony morphology

@refincubation periodmedium used
1957810-14 daysISP 2
1957810-14 daysISP 3
1957810-14 daysISP 4
1957810-14 daysISP 5
1957810-14 daysISP 6
1957810-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19578noISP 2
19578noISP 3
19578noISP 4
19578noISP 5
19578noISP 6
19578noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11240GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
11240N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium554.pdf
19578ISP 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
19578ISP 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:
19578ISP 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
19578ISP 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
19578ISP 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
19578ISP 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
11240GYM 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

culture temp

@refgrowthtypetemperaturerange
19578positiveoptimum28mesophilic
11240positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 92.981

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
19578NaClpositivemaximum5 %
69480non-halophilic97.071

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H8), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1957817234glucose+
1957822599arabinose+
1957817992sucrose+
1957818222xylose+
1957817268myo-inositol+
1957829864mannitol+
1957828757fructose+
1957826546rhamnose+
1957816634raffinose+
1957862968cellulose+
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
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
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

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19578+++-+++++++---++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19578---------+-

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_32045.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_1053;97_19059;98_23773;99_32045&stattab=map
  • Last taxonomy: Actinomadura
  • 16S sequence: AJ293706
  • Sequence Identity:
  • Total samples: 1757
  • soil counts: 1327
  • aquatic counts: 139
  • animal counts: 132
  • plant counts: 159

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
195781Risk group (German classification)
112401Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura livida strain ATCC33578 16S ribosomal RNA gene, partial sequenceAF051382108ena79909
20218Actinomadura livida strain ATCC33578 16S ribosomal RNA gene, partial sequenceAF051388191ena79909
20218Actinomadura livida partial 16S rRNA gene, strain IMSNU 22191TAJ2937061525ena79909
20218Actinomadura livida 16S ribosomal RNA gene, partial sequenceAF1631161466ena79909
20218Actinomadura livida 16S-23S ribosomal RNA intergenic spacer sequenceAF163127464ena79909

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura livida JCM 3387GCA_014648675scaffoldncbi79909
66792Actinomadura livida strain JCM 338779909.3wgspatric79909
66792Enterococcus timonensis Marseille-P2817GCA_900104595contigpatric1852364

External links

@ref: 11240

culture collection no.: DSM 43677, ATCC 33578, INA 1678, JCM 3387, CPCC 203281, IFO 14682, IMET 9575, IMSNU 20008, IMSNU 22191, MTCC 1382, NBRC 14682, VKM Ac-908

straininfo link

@refpassport
20218http://www.straininfo.net/strains/168620
20218http://www.straininfo.net/strains/124491
20218http://www.straininfo.net/strains/124492

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11240Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43677)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43677
19578Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43676.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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)