Strain identifier

BacDive ID: 16966

Type strain: Yes

Species: Actinomadura formosensis

Strain Designation: C-36820

Strain history: CIP <- 1998, JCM <- IFO <- T. Hasegawa: strain C-36820

NCBI tax ID(s): 1220557 (strain), 60706 (species)

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General

@ref: 11445

BacDive-ID: 16966

DSM-Number: 43997

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

description: Actinomadura formosensis C-36820 is an obligate aerobe, spore-forming, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
60706species
1220557strain

strain history

@refhistory
11445<- T. Hasegawa, C-36820
67770IFO 14204 <-- T. Hasegawa C-36820.
119427CIP <- 1998, JCM <- IFO <- T. Hasegawa: strain C-36820

doi: 10.13145/bacdive16966.20240916.9.1

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 formosensis
  • full scientific name: Actinomadura formosensis (Hasegawa et al. 1986) Zhang et al. 1998

  • synonyms

    • @ref: 20215
    • synonym: Thermomonospora formosensis

@ref: 11445

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura formosensis

full scientific name: Actinomadura formosensis (Hasegawa et al. 1986) Zhang et al. 1998

strain designation: C-36820

type strain: yes

Morphology

cell morphology

  • @ref: 119427
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19991Pastel orange (2003)10-14 daysISP 2
19991Antique pink (3014)10-14 daysISP 3
19991Antique pink (3014)10-14 daysISP 4
19991Antique pink (3014)10-14 daysISP 5
19991Antique pink (3014)10-14 daysISP 6
19991Antique pink (3014)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19991noISP 2
19991noISP 3
19991noISP 4
19991noISP 5
19991noISP 6
19991noISP 7

multimedia

  • @ref: 11445
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43997.jpg
  • caption: Medium 554 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11445N-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
11445GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: 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 water
19991ISP 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
19991ISP 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:
19991ISP 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
19991ISP 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
19991ISP 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
19991ISP 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
39323MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119427CIP Medium 275yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=275
119427CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
11445positivegrowth37
19991positivemaximum40
19991positiveminimum20
19991positiveoptimum37
39323positivegrowth30
67770positivegrowth28
119427positivegrowth22-41
119427nogrowth5
119427nogrowth15

Physiology and metabolism

oxygen tolerance

  • @ref: 119427
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
119427yes

compound production

@refcompound
11445rifamicins O
11445rifamicins S

halophily

@refsaltgrowthtested relationconcentration
19991NaClpositivemaximum2.5 %
119427NaClpositivegrowth0-2 %
119427NaClnogrowth4 %
119427NaClnogrowth6 %
119427NaClnogrowth8 %
119427NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1999117234glucose+
1999122599arabinose+
1999117992sucrose+
1999118222xylose+
1999117268myo-inositol+
1999129864mannitol+
1999128757fructose+
1999126546rhamnose+
1999116634raffinose+
1999162968cellulose+
68371Potassium 5-ketogluconate-builds acid from
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
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
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-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
11942716947citrate-carbon source
1194274853esculin-hydrolysis
11942717234glucose-fermentation
11942717716lactose-fermentation
11942717632nitrate+reduction
11942716301nitrite-reduction
119427132112sodium thiosulfate-builds gas from
11942717234glucose-degradation
11942717632nitrate+respiration

antibiotic resistance

  • @ref: 119427
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6777016324rifamycin Oyes
6777034948rifamycin Syes
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11942735581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11942715688acetoin-
11942717234glucose-

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
119427oxidase-
119427beta-galactosidase+3.2.1.23
119427alcohol dehydrogenase-1.1.1.1
119427gelatinase+
119427amylase-
119427DNase+
119427caseinase+3.4.21.50
119427catalase+1.11.1.6
119427tween esterase-
119427gamma-glutamyltransferase-2.3.2.2
119427lecithinase-
119427lipase-
119427lysine decarboxylase-4.1.1.18
119427ornithine decarboxylase-4.1.1.17
119427phenylalanine ammonia-lyase-4.3.1.24
119427protease+
119427tryptophan deaminase-
119427urease-3.5.1.5
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
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
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- FucosidaseControl
19991+++-++-++++--------
119427+++-++--+-+---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19991-++++-+---+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119427----+/------+++--------++/-++++/-+---+---+/-+------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119427---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11445soil
67770SoilTaipeiTaiwan, Province of ChinaTWNAsia
119427Environment, SoilChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_32455.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_1053;97_1231;98_11674;99_32455&stattab=map
  • Last taxonomy: Actinomadura formosensis
  • 16S sequence: AJ420140
  • Sequence Identity:
  • Total samples: 221
  • soil counts: 148
  • aquatic counts: 23
  • animal counts: 36
  • plant counts: 14

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
114451Risk group (German classification)
199911German classification
1194271Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura formosensis 16S rRNA gene, strain DSM 43997TAJ4201401500nuccore60706
20218Actinomadura formosensis gene for 16S ribosomal RNA, partial sequenceAB0061721474nuccore60706
20218Actinomadura formosensis partial 16S rRNA gene, strain IMSNU 22194TAJ2937031513nuccore60706
20218Thermomonospora formosensis 16S ribosomal RNA gene, partial sequenceAF0022631456nuccore60706
20218Actinomadura formosensis 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAF134096404nuccore60706

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura formosensis NBRC 142041220557.3wgspatric1220557
66792Actinomadura formosensis LMG 291782898624239draftimg60706
66792Actinomadura formosensis NBRC 142042731957572draftimg1220557
67770Actinomadura formosensis NBRC 14204GCA_001552155contigncbi1220557
67770Actinomadura formosensis OA1-2GCA_900659625contigncbi60706

GC content

  • @ref: 67770
  • GC-content: 72
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes88.8no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no89.331no
69480spore-formingspore-formingAbility to form endo- or exosporesyes87.171no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.307yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.4yes
69480flagellatedmotile2+Ability to perform flagellated movementno88.667no

External links

@ref: 11445

culture collection no.: DSM 43997, ATCC 49059, IFO 14204, JCM 7474, NBRC 14204, BCRC 16355, CIP 105595, IFO 15870, IMSNU 22194, KCTC 9647, LMG 29178, NBRC 15870, NCIMB 12773, NRRL B-16984, VKM Ac-1954

straininfo link

  • @ref: 85970
  • straininfo: 46087

literature

  • topic: Phylogeny
  • Pubmed-ID: 31310199
  • title: Actinomadura roseirufa sp. nov., producer of semduramicin, a polyether ionophore.
  • authors: Wieme AD, Gossele F, Snauwaert C, Cleenwerck I, Vandamme P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003591
  • year: 2019
  • mesh: Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Ionophores, Japan, Nigericin/*analogs & derivatives/metabolism, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11445Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43997)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43997
19991Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43997.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
39323Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17631
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
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
85970Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46087.1StrainInfo: A central database for resolving microbial strain identifiers
119427Curators of the CIPCollection of Institut Pasteur (CIP 105595)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105595