Strain identifier

BacDive ID: 16979

Type strain: Yes

Species: Actinomadura hibisca

Strain Designation: SA 26015

Strain history: NCIMB 13253 <-- ATCC 53557 <-- Bristol-Myers Co.; P157-2 (SA26015).

NCBI tax ID(s): 1220559 (strain), 68565 (species)

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General

@ref: 11525

BacDive-ID: 16979

DSM-Number: 44148

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

description: Actinomadura hibisca SA 26015 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1220559strain
68565species

strain history

@refhistory
11525<- ATCC <- Bristol-Myers Co., P157-2
67770NCIMB 13253 <-- ATCC 53557 <-- Bristol-Myers Co.; P157-2 (SA26015).

doi: 10.13145/bacdive16979.20230509.8.1

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 hibisca
  • full scientific name: Actinomadura hibisca Tomita et al. 1991

@ref: 11525

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura hibisca

full scientific name: Actinomadura hibisca Tomita et al. 1991 emend. Nouioui et al. 2018

strain designation: SA 26015

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
20006Raspberry red (3027)10-14 daysISP 2
20006Raspberry red (3027)10-14 daysISP 3
20006Raspberry red (3027)10-14 daysISP 4
20006Raspberry red (3027)10-14 daysISP 5
20006Raspberry red (3027)10-14 daysISP 6
20006Raspberry red (3027)10-14 daysISP 7

multicellular morphology

@refcomplex namecomplex colormedium nameforms multicellular complex
20006Aerial MyceliumWhiteISP 2
20006Aerial MyceliumWhiteISP 3yes
20006ISP 4no
20006ISP 5no
20006ISP 6no
20006ISP 7no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11525GYM 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
20006ISP 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
20006ISP 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:
20006ISP 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
20006ISP 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
20006ISP 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
20006ISP 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
11525PEPTON-CORN MEAL MEDIUM (DSMZ Medium 831)yeshttps://mediadive.dsmz.de/medium/831Name: PEPTON-CORN MEAL MEDIUM (DSMZ Medium 831) Composition: Corn meal agar 17.0 g/l Starch 10.0 g/l Peptone 5.0 g/l NaCl 5.0 g/l CaCl2 0.5 g/l Distilled water
11525CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
11525positivegrowth28mesophilic
20006positiveoptimum30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
20006yes
69481yes100
69480yes100

compound production

@refcompound
11525pradimicin A
11525pradimicin B
11525pradimicin M
11525pradimicin O
11525pradimicin N
11525pradimicin P
20216Pradimicin A
20216Pradimicin B
20216Pradimicin C
20006Pradimicins

halophily

  • @ref: 20006
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2000617234glucose+
2000622599arabinose+
2000617992sucrose+
2000618222xylose+
2000617268myo-inositol+
2000629864mannitol+
2000628757fructose+
2000626546rhamnose+
2000616634raffinose+
2000662968cellulose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6777083230pradimicinyes
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

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
20006+++-+++++++-+-+++-+

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20006-++++-----+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11525soil
67770SoilFijiFJIAustralia and Oceania

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3889.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_1053;97_2395;98_2958;99_3889&stattab=map
  • Last taxonomy: Actinomadura hibisca subclade
  • 16S sequence: AJ420136
  • Sequence Identity:
  • Total samples: 81
  • soil counts: 42
  • aquatic counts: 3
  • animal counts: 3
  • plant counts: 33

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115251Risk group (German classification)
200061German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura hibisca 16S rRNA gene, strain DSM 44148TAJ4201361453ena68565
20218Actinomadura hibisca partial 16S rRNA gene, strain IMSNU 22185TAJ2937051516ena68565
20218Actinomadura hibisca 16S ribosomal RNA gene, partial sequenceAF1631151457ena68565
20218Actinomadura hibisca 16S-23S ribosomal RNA intergenic spacer sequenceAF163126473ena68565

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura hibisca NBRC 151771220559.3wgspatric1220559
66792Actinomadura hibisca NBRC 151772731957594draftimg1220559
67770Actinomadura hibisca NBRC 15177GCA_001552635contigncbi1220559

GC content

  • @ref: 67770
  • GC-content: 72.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno51.166no
gram-positiveyes88.056no
anaerobicno98.743no
halophileno93.778no
spore-formingyes94.103yes
glucose-utilyes88.768yes
flagellatedno92.449no
aerobicyes90.121no
thermophileno97.67no
glucose-fermentno90.126no

External links

@ref: 11525

culture collection no.: DSM 44148, ATCC 53557, IFO 15177, NBRC 15177, NCIMB 13253, JCM 9627, HUT 6599, IMSNU 22185

straininfo link

  • @ref: 85983
  • straininfo: 125863

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity2167304Pradimicins A, B and C: new antifungal antibiotics. II. In vitro and in vivo biological activities.Oki T, Tenmyo O, Hirano M, Tomatsu K, Kamei HJ Antibiot (Tokyo)10.7164/antibiotics.43.7631990Animals, *Anthracyclines, Antibiotics, Antineoplastic/*pharmacology/therapeutic use/toxicity, Antifungal Agents/*pharmacology/therapeutic use/toxicity, Antiviral Agents/pharmacology/therapeutic use/toxicity, Cells, Cultured, Dermatomycoses/drug therapy, Female, Fungi/*drug effects, Lung Diseases, Fungal/drug therapy, Male, Mice, Mice, Inbred ICR, Mycoses/*drug therapy, Orthomyxoviridae/drug effects, Simplexvirus/drug effects, Vaginitis/drug therapy, Viral Plaque Assay
Enzymology2387770New antifungal antibiotics, pradimicins D and E. Glycine analogs of pradimicins A and C.Sawada Y, Nishio M, Yamamoto H, Hatori M, Miyaki T, Konishi M, Oki TJ Antibiot (Tokyo)10.7164/antibiotics.43.7711990Actinomycetales/genetics/*metabolism, Animals, *Anthracyclines, Antibiotics, Antineoplastic/analysis/*biosynthesis/isolation & purification/pharmacology/therapeutic use, Antifungal Agents/*biosynthesis/isolation & purification/pharmacology, Candidiasis/*drug therapy, Fermentation, Fungi/*drug effects, Magnetic Resonance Spectroscopy, Male, Mass Spectrometry, Mice, Mice, Inbred ICR, Molecular Structure, Mutation, Spectrophotometry, Ultraviolet, Yeasts/drug effectsPhylogeny
Phylogeny32845828Actinomadura rubteroloni sp. nov. and Actinomadura macrotermitis sp. nov., isolated from the gut of the fungus growing-termite Macrotermes natalensis.Benndorf R, Martin K, Kufner M, de Beer ZW, Vollmers J, Kaster AK, Beemelmanns CInt J Syst Evol Microbiol10.1099/ijsem.0.0044032020Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gastrointestinal Microbiome, Isoptera/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, South Africa, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
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
11525Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44148)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44148
20006Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44148.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
85983Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID125863.1StrainInfo: A central database for resolving microbial strain identifiers