Strain identifier

BacDive ID: 16933

Type strain: Yes

Species: Actinomadura madurae

Strain history: CIP <- 1988, JCM <- DSM <- CCM <- R.E. Gordon <- A.E. des Area Leao, Nocardia madurae

NCBI tax ID(s): 1220569 (strain), 1993 (species)

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General

@ref: 10730

BacDive-ID: 16933

DSM-Number: 43067

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

description: Actinomadura madurae DSM 43067 is an obligate aerobe, spore-forming, mesophilic human pathogen that builds an aerial mycelium and was isolated from mycetoma pedis tissue.

NCBI tax id

NCBI tax idMatching level
1993species
1220569strain

strain history

@refhistory
10730<- CCM (Nocardia madurae) <- R.E. Gordon, IMRU <- A.E. des Area Leao, Inst. Oswaldo Cruz, Rio de Janeiro
67770KCC A-0238 <-- IFO 13909 <-- IMRU 507 <-- P. Thibault.
67770DSM 43067 <-- CCM 136 <-- R. E. Gordon 1190 <-- A. E. des Area Leao.
120745CIP <- 1988, JCM <- DSM <- CCM <- R.E. Gordon <- A.E. des Area Leao, Nocardia madurae

doi: 10.13145/bacdive16933.20230509.8.1

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 madurae
  • full scientific name: Actinomadura madurae (Vincent 1894) Lechevalier and Lechevalier 1970 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Streptothrix madurae

@ref: 10730

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura madurae

full scientific name: Actinomadura madurae (Vincent 1894) Lechevalier and Lechevalier 1970 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120745positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19936Beige (1001)10-14 daysISP 2
19936Beige (1001)10-14 daysISP 3
19936Beige (1001)10-14 daysISP 4
19936Beige (1001)10-14 daysISP 5
19936Beige (1001)10-14 daysISP 6
19936Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19936yesAerial MyceliumWhiteISP 2
19936noISP 3
19936noISP 4
19936noISP 5
19936noISP 6
19936noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19936ISP 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
19936ISP 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:
19936ISP 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
19936ISP 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
19936ISP 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
19936ISP 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
39304MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
10730GLYCEROL-SOIL MEDIUM (DSMZ Medium 80)yesName: GLYCEROL-SOIL MEDIUM (DSMZ Medium 80) Composition: Glycerol 20.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Beef extract 3.0 g/l Soil extract Distilled waterhttps://mediadive.dsmz.de/medium/80
10730GYM 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
120745CIP Medium 236yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=236
120745CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120745CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19936positiveoptimum37mesophilic
39304positivegrowth37mesophilic
10730positivegrowth37mesophilic
67770positivegrowth37mesophilic
120745positivegrowth22-41
120745nogrowth5psychrophilic
120745nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120745
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.128

compound production

@refcompound
10730nonyl prodigiosine
10730undecyl prodigiosine
19936Maduropeptin
19936Prodiogisine
19936Simaomicin

halophily

@refsaltgrowthtested relationconcentration
19936NaClpositivemaximum2.5 %
120745NaClpositivegrowth0-2 %
120745NaClnogrowth4 %
120745NaClnogrowth6 %
120745NaClnogrowth8 %
120745NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1993662968cellulose-
1993616634raffinose-
1993626546rhamnose-
1993628757fructose+
1993629864mannitol-
1993617268myo-inositol-
1993618222xylose+
1993617992sucrose-
1993622599arabinose+
1993617234glucose+
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
1207454853esculin+hydrolysis
12074517632nitrate+reduction
12074516301nitrite-reduction
12074517234glucose+degradation
12074517632nitrate-respiration

antibiotic resistance

  • @ref: 120745
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12074535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12074515688acetoin-
12074517234glucose-

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
120745oxidase-
120745beta-galactosidase-3.2.1.23
120745alcohol dehydrogenase+1.1.1.1
120745gelatinase+
120745amylase-
120745DNase-
120745caseinase+3.4.21.50
120745catalase+1.11.1.6
120745tween esterase-
120745gamma-glutamyltransferase+2.3.2.2
120745lecithinase-
120745lipase-
120745lysine decarboxylase-4.1.1.18
120745ornithine decarboxylase-4.1.1.17
120745phenylalanine ammonia-lyase-4.3.1.24
120745tryptophan deaminase-
120745urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    51271C14:02.814
    51271C15:01.115
    51271C16:035.716
    51271C17:01.717
    51271C18:04.718
    51271C16:0 iso4.415.626
    51271C16:1 ω7c6.915.819
    51271C16:1 ω9c2.115.774
    51271C17:0 10-methyl1.417.41
    51271C17:1 ω8c1.716.792
    51271C18:1 ω9c2517.769
    51271C18:2 ω6,9c/C18:0 ANTE2.517.724
    51271TBSA 10Me18:010.118.392
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19936+-+-+---+++----+---
120745+++-+++-+-+---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19936----------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120745---+/--+/--+/---+/----+/---+/----+/---+/--+/----------------------+/-

Isolation, sampling and environmental information

isolation

@refsample type
10730mycetoma pedis tissue
51271Human foot,mycetoma
67770Mycetoma of foot
120745Mycetoma of foot

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host Body-Site#Limb#Foot

taxonmaps

  • @ref: 69479
  • File name: preview.99_5613.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_1053;97_1231;98_1478;99_5613&stattab=map
  • Last taxonomy: Actinomadura madurae
  • 16S sequence: X97889
  • Sequence Identity:
  • Total samples: 118
  • soil counts: 113
  • aquatic counts: 2
  • animal counts: 3

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
10730yesyes2Risk group (German classification)
199362German classification
1207452Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura madurae clone B1 16S ribosomal RNA gene, partial sequenceAY262334502ena1993
20218A.madurae 16S rRNA geneX978891445ena1993
20218Actinomadura madurae gene for 16S ribosomal RNA, partial sequenceD854681469ena1993
20218Actinomadura madurae 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAF134103455ena1993
20218Actinomadura madurae DNA for 16S rRNA, partial sequenceD506681341ena1993
20218Actinomadura madurae 16S ribosomal RNA gene sequenceU585271440ena1993

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura madurae strain DSM 430671993.7wgspatric1993
66792Actinomadura madurae DSM 430672634166331draftimg1993
67770Actinomadura madurae DSM 43067GCA_900115095scaffoldncbi1993

GC content

@refGC-contentmethod
6777072.1genome sequence analysis
6777068.2thermal denaturation, midpoint method (Tm)
6777068thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.699no
gram-positiveyes87.978no
anaerobicno98.782no
aerobicyes89.619no
halophileno88.171no
spore-formingyes94.123no
glucose-utilyes89.58yes
flagellatedno97.871no
thermophileno93.066yes
glucose-fermentno90.493no

External links

@ref: 10730

culture collection no.: DSM 43067, ATCC 19425, CCM 136, IAM 14277, IFO 14623, IMRU 1190, JCM 7436, NBRC 14623, NCTC 5654, CCUG 32944, CCTCC AB 2010169, CECT 3043, CGMCC 4.1224, CIP 105487, HAMBI 1926, IFM 0585, IMET 9585, KCTC 9192, MTCC 1120, NCIMB 13469, NRRL B-3843, VKM Ac-809, IFO 13909, NBRC 13909

straininfo link

  • @ref: 85938
  • straininfo: 36984

literature

  • topic: Phylogeny
  • Pubmed-ID: 25678680
  • title: Actinomadura darangshiensis sp. nov., isolated from a volcanic cone.
  • authors: Lee SD, Kim SB
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.000099
  • year: 2015
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, Volcanic Eruptions
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10730Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43067)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43067
19936Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43067.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
39304Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17512
51271Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32944)https://www.ccug.se/strain?id=32944
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
85938Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36984.1StrainInfo: A central database for resolving microbial strain identifiers
120745Curators of the CIPCollection of Institut Pasteur (CIP 105487)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105487