Strain identifier

BacDive ID: 16932

Type strain: Yes

Species: Actinomadura macra

Strain Designation: FD 25934, A-0287

Strain history: CIP <- 1998, JCM <- KCC: strain A-0287 <- Chas, Pfizer & Co.: strain FD 25934

NCBI tax ID(s): 1220564 (strain), 46164 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 11344

BacDive-ID: 16932

DSM-Number: 43862

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

description: Actinomadura macra FD 25934 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
46164species
1220564strain

strain history

@refhistory
11344<- JCM <- KCC <- Chas. Pfizer & Co., FD 25934
67770KCC A-0287 <-- Chas. Pfizer & Co.; FD 25934.
120741CIP <- 1998, JCM <- KCC: strain A-0287 <- Chas, Pfizer & Co.: strain FD 25934

doi: 10.13145/bacdive16932.20230509.8.1

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 macra
  • full scientific name: Actinomadura macra (ex Celmer et al. 1979) Huang 1980

@ref: 11344

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura macra

full scientific name: Actinomadura macra (ex Celmer et al. 1979) Huang 1980 emend. Nouioui et al. 2018

strain designation: FD 25934, A-0287

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120741positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19972Red brown (8012)10-14 daysISP 2
19972Colorless10-14 daysISP 3
19972Colorless10-14 daysISP 4
19972Beige (1001)10-14 daysISP 5
19972Beige (1001)10-14 daysISP 6
19972Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19972yesAerial MyceliumWhiteISP 2
19972noISP 3
19972noISP 4
19972noISP 5
19972noISP 6
19972noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19972ISP 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
19972ISP 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:
19972ISP 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
19972ISP 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
19972ISP 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
19972ISP 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
34048MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
11344GYM 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
120741CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116
120741CIP Medium 194yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=194

culture temp

@refgrowthtypetemperaturerange
19972positiveoptimum28mesophilic
34048positivegrowth30mesophilic
11344positivegrowth28mesophilic
67770positivegrowth28mesophilic
120741positivegrowth25-37mesophilic
120741nogrowth5psychrophilic
120741nogrowth15psychrophilic
120741nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120741
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
20216Antibiotic CP 47433
20216Antibiotic CP 47434
19972Polyether antibiotic, active against gram-positive, shows anticoccidial activity
67770Antibiotics CP-47433 and CP-47434

halophily

@refsaltgrowthtested relationconcentration
19972NaClpositivemaximum2.5 %
120741NaClpositivegrowth0 %
120741NaClnogrowth2 %
120741NaClnogrowth4 %
120741NaClnogrowth6 %
120741NaClnogrowth8 %
120741NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1997217234glucose+
1997222599arabinose-
1997217992sucrose-
1997218222xylose-
1997217268myo-inositol-
1997229864mannitol-
1997228757fructose-
1997226546rhamnose-
1997216634raffinose-
1997262968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1207414853esculin-hydrolysis
12074117632nitrate+reduction
12074116301nitrite-reduction
12074117632nitrate-respiration

antibiotic resistance

  • @ref: 120741
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12074135581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12074115688acetoin-
12074117234glucose-

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
120741oxidase-
120741beta-galactosidase-3.2.1.23
120741alcohol dehydrogenase-1.1.1.1
120741gelatinase-
120741catalase+1.11.1.6
120741gamma-glutamyltransferase+2.3.2.2
120741lysine decarboxylase-4.1.1.18
120741ornithine decarboxylase-4.1.1.17
120741phenylalanine ammonia-lyase-4.3.1.24
120741tryptophan deaminase-
120741urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382acid phosphatase-3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382beta-glucosidase-3.2.1.21
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
19972--++++--+-----+-+--
120741-++-+-----+---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19972-++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11344soilOkayamaJapanJPNAsia
67770SoilOkayamaJapanJPNAsia
120741Environment, SoilOkayamaJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3797.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_1053;97_1231;98_2893;99_3797&stattab=map
  • Last taxonomy: Actinomadura
  • 16S sequence: U49009
  • Sequence Identity:
  • Total samples: 79
  • soil counts: 72
  • aquatic counts: 4
  • animal counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113441Risk group (German classification)
199721German classification
1207411Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura macra 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAF134102450ena46164
20218Actinomadura macra 16S rRNA geneU490091403ena46164
20218Actinomadura macra gene for 16S rRNA, partial sequence, strain: NBRC 14102AB3645941471ena46164

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura macra NBRC 141021220564.3wgspatric1220564
66792Actinomadura macra NBRC 141022731957575draftimg1220564
67770Actinomadura macra NBRC 14102GCA_001552215contigncbi1220564

GC content

  • @ref: 67770
  • GC-content: 70.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno91.418no
gram-positiveyes89.45no
anaerobicno98.501no
aerobicyes88.749no
halophileno92.368no
spore-formingyes92.928no
thermophileno92.36no
glucose-utilyes90.984yes
flagellatedno97.997no
glucose-fermentno87.275no

External links

@ref: 11344

culture collection no.: DSM 43862, ATCC 31286, IFO 14102, IMET 9754, JCM 3287, KCC A-0287, NBRC 14102, BCC 49509, BCRC 13378, CGMCC 4.1513, CIP 105532, IMSNU 22164, KCTC 9342, MTCC 2559, NCIMB 14303, NRRL B-16124, TBRC 2223

straininfo link

  • @ref: 85937
  • straininfo: 39984

literature

  • topic: Phylogeny
  • Pubmed-ID: 33616515
  • title: Actinomadura litoris sp. nov., an actinobacterium isolated from sandy soil in Sanya.
  • authors: Cao P, Xu X, Li C, Han L, Mu W, Xiang W, Zhao J, Wang X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.004708
  • year: 2021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11344Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43862)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43862
19972Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43862.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
34048Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17562
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
85937Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39984.1StrainInfo: A central database for resolving microbial strain identifiers
120741Curators of the CIPCollection of Institut Pasteur (CIP 105532)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105532