Strain identifier

BacDive ID: 16931

Type strain: Yes

Species: Actinomadura luteofluorescens

Strain Designation: S-0203

Strain history: CIP <- 1998, JCM <- KCC: strain S-0203 <- R. Shinobu: strain 719, Streptomyces luteofluorescens

NCBI tax ID(s): 46163 (species)

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General

@ref: 9521

BacDive-ID: 16931

DSM-Number: 40398

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

description: Actinomadura luteofluorescens S-0203 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 46163
  • Matching level: species

strain history

@refhistory
9521<- E.B. Shirling, ISP (Streptomyces luteofluorescens) <- R. Shinobu, OEU 719
67770KCC S-0203 <-- R. Shinobu 719.
120688CIP <- 1998, JCM <- KCC: strain S-0203 <- R. Shinobu: strain 719, Streptomyces luteofluorescens

doi: 10.13145/bacdive16931.20230509.8.1

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 luteofluorescens
  • full scientific name: Actinomadura luteofluorescens (Shinobu 1962) Preobrazhenskaya et al. 1975 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces luteofluorescens

@ref: 9521

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura luteofluorescens

full scientific name: Actinomadura luteofluorescens (Shinobu 1962) Preobrazhenskaya et al. 1975

strain designation: S-0203

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120688positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19450Salmon orange10-14 daysISP 2
19450Yellow10-14 daysISP 3
19450Yellow10-14 daysISP 4
19450Beige10-14 daysISP 5
19450Beige10-14 daysISP 6
19450Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19450noISP 2
19450yesISP 3Aerial MyceliumWhite
19450noISP 4
19450yesISP 5Aerial MyceliumWhite
19450yesISP 6Aerial MyceliumWhite
19450noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9521N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium554.pdf
19450ISP 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
19450ISP 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:
19450ISP 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
19450ISP 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
19450ISP 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
19450ISP 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
39302MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
9521GYM 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
120688CIP Medium 236yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=236
120688CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19450positiveoptimum28mesophilic
39302positivegrowth30mesophilic
9521positivegrowth28mesophilic
67770positivegrowth28mesophilic
120688positivegrowth22-41
120688nogrowth5psychrophilic
120688nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120688
  • oxygen tolerance: obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
19450Formation of spore chains: hooks, spore surface: smoothsporeyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
19450NaClpositivemaximum5 %
120688NaClpositivegrowth0-4 %
120688NaClnogrowth6 %
120688NaClnogrowth8 %
120688NaClnogrowth10 %

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
1945062968cellulose-
1945016634raffinose-
1945026546rhamnose+
1945028757fructose+
1945029864mannitol+
1945017268myo-inositol+
1945018222xylose+
1945017992sucrose+
1945022599arabinose+
1945017234glucose+
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
6837128017starch+builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose+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
1206884853esculin-hydrolysis
12068817632nitrate+reduction
12068816301nitrite-reduction
12068817234glucose+/-degradation
12068817632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12068835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12068815688acetoin-
12068817234glucose-

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
120688oxidase-
120688beta-galactosidase+3.2.1.23
120688alcohol dehydrogenase-1.1.1.1
120688gelatinase+
120688amylase-
120688DNase-
120688caseinase+3.4.21.50
120688catalase+1.11.1.6
120688tween esterase-
120688gamma-glutamyltransferase+2.3.2.2
120688lecithinase+
120688lipase-
120688lysine decarboxylase-4.1.1.18
120688ornithine decarboxylase-4.1.1.17
120688phenylalanine ammonia-lyase-4.3.1.24
120688protease+
120688tryptophan deaminase-
120688urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin+3.4.21.4
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
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
19450+++-+++++++---+-+--
120688++++++-+-++-----+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19450---------++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120688----+/------+++--------++/-++-++/---+/-+---++--+---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9521soil
67770SoilNoheji City, Aomori Pref.JapanJPNAsia
120688Environment, SoilAomoriJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
95211Risk group (German classification)
194501Risk group (German classification)
1206881Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura luteofluorescens 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAF134101533ena46163
20218Actinomadura luteofluorescens gene for 16S ribosomal RNA, partial sequence, strain: JCM 4203D44029120ena46163
9521Actinomadura luteofluorescens 16S rRNA geneU490081409ena46163

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura luteofluorescens strain DSM 4039846163.3wgspatric46163
66792Actinomadura luteofluorescens DSM 403982844792859draftimg46163
67770Actinomadura luteofluorescens DSM 40398GCA_013409365contigncbi46163

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.458no
anaerobicno98.448no
halophileno89.219no
spore-formingyes92.14yes
glucose-utilyes88.29yes
aerobicyes89.458no
flagellatedno97.812no
thermophileno97.041yes
motileno92.557no
glucose-fermentno88.029no

External links

@ref: 9521

culture collection no.: DSM 40398, ATCC 25469, CBS 702.69, CGMCC AS 4.1382, IFO 13057, ISP 5398, JCM 4203, KCC S-0203, KCC S-0491, NBRC 13057, RIA 1249, OEU 719, BCRC 16250, CECT 3283, CGMCC 4.1382, CGMCC 4.1516, CIP 105484, IMET 9672, IMSNU 20009, JCM 4491, KCTC 9341, NRRL B-12327, VKM Ac-1509

straininfo link

  • @ref: 85936
  • straininfo: 389484

literature

  • topic: Phylogeny
  • Pubmed-ID: 1160657
  • title: [Systematic position of Streptomyces luteofluorescens].
  • authors: Preobrazhenskaia TP, Lavrova NV, Blinov NO
  • journal: Mikrobiologiia
  • year: 1975
  • mesh: Cell Wall/analysis, Diaminopimelic Acid/analysis, Polysaccharides, Bacterial/analysis, Streptomyces/analysis/*classification

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9521Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40398)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40398
19450Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40398.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
39302Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17508
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
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
85936Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389484.1StrainInfo: A central database for resolving microbial strain identifiers
120688Curators of the CIPCollection of Institut Pasteur (CIP 105484)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105484