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Strain identifier

BacDive ID: 16986

Type strain: Yes

Species: Actinomadura namibiensis

Strain Designation: FH-A 1198, ID 90-506

Strain history: DSM 44197 <-- J. Wink FH-A 1198 (=HAG 010767).

NCBI tax ID(s): 182080 (species)

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

@ref: 11593

BacDive-ID: 16986

DSM-Number: 44197

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

description: Actinomadura namibiensis FH-A 1198 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil sample.

NCBI tax id

  • NCBI tax id: 182080
  • Matching level: species

strain history

doi: 10.13145/bacdive16986.20221219.7.1

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 namibiensis
  • full scientific name: Actinomadura namibiensis Wink et al. 2003

@ref: 11593

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura namibiensis

full scientific name: Actinomadura namibiensis Wink et al. 2003

strain designation: FH-A 1198, ID 90-506

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 91.987

colony morphology

@refcolony colorincubation periodmedium used
20016Salmon pink (3022)10-14 daysISP 2
20016Salmon pink (3022)10-14 daysISP 3
20016Salmon pink (3022)10-14 daysISP 4
20016Salmon pink (3022)10-14 daysISP 5
20016Colorless10-14 daysISP 6
20016Salmon pink (3022)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
20016noISP 2
20016noISP 3
20016yesISP 4Aerial MyceliumWhite
20016noISP 5
20016noISP 6
20016noISP 7

multimedia

  • @ref: 11593
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44197.jpg
  • caption: Medium 554 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11593ROLLED 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
11593GYM 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
20016ISP 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
20016ISP 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:
20016ISP 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
20016ISP 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
20016ISP 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
20016ISP 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
33952MEDIUM 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)
11593N-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

culture temp

@refgrowthtypetemperaturerange
11593positivegrowth28mesophilic
20016positiveoptimum28mesophilic
33952positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
20016Formation of spore chains (spirales)(Sp), spore surface smoothyes
69480yes98.795

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
20016NaClpositivegrowth0 %
69480non-halophilic96.351

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2001617234glucose+
2001622599arabinose+
2001617992sucrose+
2001618222xylose+/-
2001617268myo-inositol+/-
2001629864mannitol+/-
2001628757fructose-
2001626546rhamnose+
2001616634raffinose-
2001662968cellulose-
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
20016+-+-+++++++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20016++--+-+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11593soil sampleNamibiaSouth AfricaZAFAfrica
67770SoilNamib DesertNamibiaNAMAfrica

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5268.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_2558;97_3127;98_3927;99_5268&stattab=map
  • Last taxonomy: Actinomadura
  • 16S sequence: AJ420134
  • Sequence Identity:
  • Total samples: 456
  • soil counts: 336
  • aquatic counts: 35
  • animal counts: 38
  • plant counts: 47

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115931Risk group (German classification)
200161German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura sp. NTRHn4 gene for 16S ribosomal RNA, partial sequenceAB9206031336ena1571739
11593Actinomadura namibiensis 16S rRNA gene, strain DSM 44197TAJ4201341438ena182080

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura namibiensis DSM 44197GCA_014138665scaffoldncbi182080
66792Actinomadura namibiensis strain DSM 44197182080.3wgspatric182080
66792Actinomadura namibiensis DSM 441972861542065draftimg182080

External links

@ref: 11593

culture collection no.: DSM 44197, CIP 108365, NRRL B-24153, HAG 010767, JCM 13238, CPCC 201670

straininfo link

@refpassport
20218http://www.straininfo.net/strains/278354
20218http://www.straininfo.net/strains/534424
20218http://www.straininfo.net/strains/401055
20218http://www.straininfo.net/strains/301757

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12807192Actinomadura namibiensis sp. nov.Wink J, Kroppenstedt RM, Seibert G, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.02286-02003Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, DNA, Ribosomal, *Desert Climate, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Spores, BacterialGenetics
Phylogeny35816443Actinomadura parmotrematis sp. nov., isolated from the foliose lichen, Parmotrema praesorediosum (Nyl.) Hale.Somphong A, Poengsungnoen V, Buaruang K, Suriyachadkun C, Sripreechasak P, Tanasupawat S, Phongsopitanun WInt J Syst Evol Microbiol10.1099/ijsem.0.0054472022Actinomadura, *Actinomycetales, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Lichens, Parmeliaceae, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11593Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44197)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44197
20016Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44197.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
33952Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5979
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)