Strain identifier

BacDive ID: 16927

Type strain: Yes

Species: Actinomadura cremea

Strain history: KCC A-0308 <-- IFO 14182 <-- ATCC 33577 <-- INA 292.

NCBI tax ID(s): 1991 (species)

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General

@ref: 11239

BacDive-ID: 16927

DSM-Number: 43676

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

description: Actinomadura cremea DSM 43676 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium.

NCBI tax id

  • NCBI tax id: 1991
  • Matching level: species

strain history

@refhistory
11239<- N.S. Agre, INA
67770KCC A-0308 <-- IFO 14182 <-- ATCC 33577 <-- INA 292.

doi: 10.13145/bacdive16927.20230509.8.1

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 cremea
  • full scientific name: Actinomadura cremea Preobrazhenskaya et al. 1975 (Approved Lists 1980)

@ref: 11239

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura cremea subsp. cremea

full scientific name: Actinomadura cremea subsp. cremea (Preobrazhenskaya et al. 1975) Gauze et al. 1987

type strain: yes

Morphology

cell morphology

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

colony morphology

@refincubation periodmedium used
1957910-14 daysISP 2
1957910-14 daysISP 3
1957910-14 daysISP 4
1957910-14 daysISP 5
1957910-14 daysISP 6
1957910-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19579noISP 2
19579yesISP 3Aerial MyceliumWhite
19579yesISP 4Aerial Mycelium
19579yesISP 5Aerial MyceliumPink
19579yesISP 6Aerial MyceliumWhite
19579yesISP 7Aerial Mycelium

multimedia

  • @ref: 11239
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43676.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19579ISP 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
19579ISP 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:
19579ISP 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
19579ISP 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
19579ISP 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
19579ISP 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
11239GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yesName: 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 waterhttps://mediadive.dsmz.de/medium/65
11239N-Z-AMINE-MEDIUM (DSMZ Medium 554)yesName: 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 waterhttps://mediadive.dsmz.de/medium/554
11239GPHF-MEDIUM (DSMZ Medium 553)yesName: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled waterhttps://mediadive.dsmz.de/medium/553

culture temp

@refgrowthtypetemperaturerange
19579positiveoptimum28mesophilic
11239positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 19579
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1957917234glucose-
1957922599arabinose+
1957917992sucrose+
1957918222xylose-
1957917268myo-inositol-
1957929864mannitol-
1957928757fructose-
1957926546rhamnose-
1957916634raffinose-
1957962968cellulose-
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
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
19579+-+++++-+++--++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19579---+--+--++

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112391Risk group (German classification)
195791Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura cremea subsp. cremea strain ATCC33577 16S ribosomal RNA gene, partial sequenceAF051379118ena31961
20218Actinomadura cremea subsp. cremea 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAF134094397ena31961
20218Actinomadura cremea subsp. cremea gene for 16S ribosomal RNA, partial sequenceAB4622911436ena31961
11239Actinomadura cremea subsp. cremea 16S ribosomal RNA gene, partial sequenceAF1340671432ena31961

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura cremea JCM 3308GCA_014648495scaffoldncbi1991
66792Actinomadura cremea strain JCM 33081991.3wgspatric1991

GC content

  • @ref: 67770
  • GC-content: 68
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.427no
gram-positiveyes87.125no
anaerobicno97.953no
aerobicyes87.386no
halophileno87.56no
spore-formingyes94.073no
thermophileno97.27yes
glucose-utilyes86.82yes
motileno92.429no
glucose-fermentno89.494no

External links

@ref: 11239

culture collection no.: DSM 43676, ATCC 33577, INA 292, JCM 3308, BCRC 13394, IFO 14182, IMET 9578, IMSNU 22199, NBRC 14182, NRRL B-16605, VKM Ac-912

straininfo link

  • @ref: 85932
  • straininfo: 40568

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics2070791Structural features of cell wall teichoic acid and peptidoglycan of Actinomadura cremea INA 292.Potekhina NV, Naumova IB, Shashkov AS, Terekhova LPEur J Biochem10.1111/j.1432-1033.1991.tb16126.x1991Actinomycetales/*analysis, Carbohydrate Conformation, Carbohydrate Sequence, Cell Wall/chemistry, Isomerism, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Peptidoglycan/*chemistry/isolation & purification, Teichoic Acids/*chemistry/isolation & purificationEnzymology
Phylogeny20952541Actinomadura apis sp. nov., isolated from a honey bee (Apis mellifera) hive, and the reclassification of Actinomadura cremea subsp. rifamycini Gauze et al. 1987 as Actinomadura rifamycini (Gauze et al. 1987) sp. nov., comb. nov.Promnuan Y, Kudo T, Ohkuma M, Chantawannakul PInt J Syst Evol Microbiol10.1099/ijs.0.026633-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Animals, Bacterial Typing Techniques, Bees/*microbiology, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Urticaria/*microbiologyGenetics
Phylogeny21705447Actinomadura sediminis sp. nov., a marine actinomycete isolated from mangrove sediment.He J, Xu Y, Sahu MK, Tian XP, Nie GX, Xie Q, Zhang S, Sivakumar K, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.032979-02011Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Carbohydrates/analysis, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, *Environmental Microbiology, Fatty Acids/analysis, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytologyGenetics
Phylogeny26542839Actinomadura algeriensis sp. nov., an actinobacterium isolated from Saharan soil.Lahoum A, Bouras N, Mathieu F, Schumann P, Sproer C, Klenk HP, Sabaou NAntonie Van Leeuwenhoek10.1007/s10482-015-0617-x2015Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Algeria, Cell Wall/metabolism, Cluster Analysis, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/metabolism, Fatty Acids/analysis, Molecular Sequence Data, Mycelium/cytology, Nucleic Acid Hybridization, Phospholipids/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Vitamin K 2/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11239Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43676)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43676
19579Wink, 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
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
85932Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40568.1StrainInfo: A central database for resolving microbial strain identifiers