Strain identifier

BacDive ID: 16990

Type strain: Yes

Species: Actinomadura napierensis

Strain Designation: B60

Strain history: DSM 44846 <-- P. R. Meyers B60 <-- M. le Roes.

NCBI tax ID(s): 267854 (species)

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General

@ref: 12027

BacDive-ID: 16990

DSM-Number: 44846

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

description: Actinomadura napierensis B60 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 267854
  • Matching level: species

strain history

@refhistory
12027<- P. R. Meyers, Univ. of Cape Town; B60 <- M. Le Roes
67770DSM 44846 <-- P. R. Meyers B60 <-- M. le Roes.

doi: 10.13145/bacdive16990.20230509.8.1

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 napierensis
  • full scientific name: Actinomadura napierensis Cook et al. 2005

@ref: 12027

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura napierensis

full scientific name: Actinomadura napierensis Cook et al. 2005

strain designation: B60

type strain: yes

Morphology

cell morphology

  • @ref: 31343
  • gram stain: positive

colony morphology

@refcolony colorincubation periodmedium used
20132Beige (1001)10-14 daysISP 2
20132Beige (1001)10-14 daysISP 3
20132Beige (1001)10-14 daysISP 4
20132Beige (1001)10-14 daysISP 5
20132Beige (1001)10-14 daysISP 6
20132Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20132yesAerial MyceliumCreamISP 2
20132yesAerial MyceliumCreamISP 3
20132yesAerial MyceliumCreamISP 4
20132yesAerial MyceliumCreamISP 5
20132yesAerial MyceliumCreamISP 6
20132noISP 7

pigmentation

  • @ref: 31343
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12027ROLLED 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
12027MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
20132ISP 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
20132ISP 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:
20132ISP 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
20132ISP 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
20132ISP 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
20132ISP 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
12027ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
12027positivegrowth28mesophilic
20132positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 31343
  • spore formation: yes

halophily

  • @ref: 31343
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2 %

observation

  • @ref: 31343
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2013217234glucose-
2013222599arabinose-
2013217992sucrose-
2013218222xylose-
2013217268myo-inositol-
2013229864mannitol-
2013228757fructose-
2013226546rhamnose+/-
2013216634raffinose+
2013262968cellulose-
3134315963ribitol+carbon source
3134322599arabinose+carbon source
3134323652dextrin+carbon source
3134328757fructose+carbon source
3134328260galactose+carbon source
3134317234glucose+carbon source
3134317754glycerol+carbon source
3134317306maltose+carbon source
3134329864mannitol+carbon source
3134337684mannose+carbon source
3134316634raffinose+carbon source
3134326546rhamnose+carbon source
3134333942ribose+carbon source
3134317992sucrose+carbon source
3134327082trehalose+carbon source
3134353426tween 80+carbon source
3134316199urea+carbon source
3134318222xylose+carbon source
313434853esculin+hydrolysis

metabolite production

  • @ref: 31343
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
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
20132-++-++---+----++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12027soilNapierSouth AfricaZAFAfrica
67770Cultivated soilNapier, Western Cape ProvinceSouth AfricaZAFAfrica

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120271Risk group (German classification)
201321German classification

Sequence information

16S sequences

  • @ref: 31343
  • description: Actinomadura napierensis 16S ribosomal RNA gene, partial sequence
  • accession: AY568292
  • length: 1346
  • database: nuccore
  • NCBI tax ID: 267854

GC content

@refGC-contentmethod
1202770.0
3134370
6777070thermal denaturation, midpoint method (Tm)

External links

@ref: 12027

culture collection no.: DSM 44846, JCM 13850, NRRL B-24319, NBRC 104150

straininfo link

  • @ref: 85993
  • straininfo: 137989

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774647Actinomadura napierensis sp. nov., isolated from soil in South Africa.Cook AE, Roes ML, Meyers PRInt J Syst Evol Microbiol10.1099/ijs.0.63359-02005Actinomycetales/*chemistry/*classification/genetics/isolation & purification, Anti-Bacterial Agents/*biosynthesis/pharmacology, Bacteria/drug effects, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Microbial Sensitivity Tests, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, South AfricaGenetics
Phylogeny22523172Actinomadura xylanilytica sp. nov., an actinomycete isolated from soil.Zucchi TD, Kim BY, Bonda ANV, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.042325-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Carbohydrates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12027Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44846)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44846
20132Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44846.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
31343Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2765728776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
85993Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID137989.1StrainInfo: A central database for resolving microbial strain identifiers