Strain identifier

BacDive ID: 16995

Type strain: Yes

Species: Actinomadura alba

Strain history: CIP <- 2008, DSMZ <- S.K. Tang, YIM <- Y.X. Wang, Yunnan Univ., Yunnan, China: strain YIM 45681

NCBI tax ID(s): 406431 (species)

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General

@ref: 12272

BacDive-ID: 16995

DSM-Number: 45045

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

description: Actinomadura alba DSM 45045 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 406431
  • Matching level: species

strain history

@refhistory
12272<- S.-K. Tang, YIM <- Y.-X. Wang
67770DSM 45045 <-- Y.-X. Wang et al. YIM 45681.
116176CIP <- 2008, DSMZ <- S.K. Tang, YIM <- Y.X. Wang, Yunnan Univ., Yunnan, China: strain YIM 45681

doi: 10.13145/bacdive16995.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinomadura
  • species: Actinomadura alba
  • full scientific name: Actinomadura alba Wang et al. 2007

@ref: 12272

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura alba

full scientific name: Actinomadura alba Wang et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
32041positive
116176positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19903Beige10-14 daysISP 2
19903Beige10-14 daysISP 3
19903Beige10-14 daysISP 4
19903Cream10-14 daysISP 5
19903Cream10-14 daysISP 6
19903Cream10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19903noISP 2
19903noISP 3
19903noISP 4
19903noISP 5
19903noISP 6
19903noISP 7

pigmentation

  • @ref: 32041
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12272GYM 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
12272GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
19903ISP 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
19903ISP 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:
19903ISP 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
19903ISP 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
19903ISP 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
19903ISP 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
37850MEDIUM 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)
116176CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
12272positivegrowth28mesophilic
32041positiveoptimum28mesophilic
37850positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 32041
  • ability: positive
  • type: optimum
  • pH: 7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32041aerobe
116176obligate aerobe

spore formation

  • @ref: 32041
  • spore formation: yes

observation

@refobservation
32041aggregates in chains
67770quinones: MK-9(H4), MK-9(H6), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1990317234glucose+
1990322599arabinose-
1990317992sucrose-
1990318222xylose-
1990317268myo-inositol-
1990329864mannitol-
1990328757fructose+
1990326546rhamnose-
1990316634raffinose-
1990362968cellulose-
3204115963ribitol+carbon source
3204118403L-arabitol+carbon source
3204128757fructose+carbon source
320415291gelatin+carbon source
3204117716lactose+carbon source
3204133942ribose+carbon source
3204117992sucrose+carbon source
3204127082trehalose+carbon source
3204118222xylose+carbon source
320414853esculin+hydrolysis
3204117632nitrate+reduction
11617617632nitrate+reduction
11617616301nitrite-reduction

metabolite production

  • @ref: 116176
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32041catalase+1.11.1.6
32041gelatinase+
32041urease+3.5.1.5
116176oxidase-
116176catalase+1.11.1.6
116176urease-3.5.1.5
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
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- FucosidaseControl
19903-------------------
116176++++++--+++---+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12272soilYunnan ProvinceChinaCHNAsia
67770Soil in a suburb of KunmingYunnan Province, south-west ChinaChinaCHNAsia
116176Environment, SoilYunnanChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_77595.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_32803;97_41536;98_54210;99_77595&stattab=map
  • Last taxonomy: Actinomadura alba subclade
  • 16S sequence: DQ985164
  • Sequence Identity:
  • Total samples: 1052
  • soil counts: 966
  • aquatic counts: 38
  • animal counts: 12
  • plant counts: 36

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
122721Risk group (German classification)
199031Risk group (German classification)
1161761Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12272
  • description: Actinomadura alba strain YIM 45681 16S ribosomal RNA gene, partial sequence
  • accession: DQ985164
  • length: 1457
  • database: ena
  • NCBI tax ID: 406431

GC content

  • @ref: 12272
  • GC-content: 66.5

External links

@ref: 12272

culture collection no.: DSM 45045, CCTCC AA 206005, CIP 109812, JCM 14906, NBRC 103884, YIM 45681

straininfo link

  • @ref: 85997
  • straininfo: 293691

literature

  • topic: Phylogeny
  • Pubmed-ID: 17684247
  • title: Actinomadura alba sp. nov., isolated from soil in Yunnan, China.
  • authors: Wang YX, Zhi XY, Chen HH, Zhang YQ, Tang SK, Jiang CL, Xu LH, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64864-0
  • year: 2007
  • mesh: Actinomycetales/chemistry/classification/genetics/*isolation & purification, Carbohydrates/analysis, Cell Wall/chemistry, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12272Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45045)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45045
19903Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45045.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
32041Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2829128776041
37850Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7597
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
85997Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID293691.1StrainInfo: A central database for resolving microbial strain identifiers
116176Curators of the CIPCollection of Institut Pasteur (CIP 109812)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109812