Strain identifier

BacDive ID: 16924

Type strain: Yes

Species: Actinomadura atramentaria

Strain Designation: SF2197

Strain history: CIP <- 2002, S. Miyadoh, Meiji Seika Kaisha Ltd., Kanagawa, Japan: strain SF2197

NCBI tax ID(s): 1120936 (strain), 1990 (species)

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General

@ref: 11270

BacDive-ID: 16924

DSM-Number: 43919

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

description: Actinomadura atramentaria SF2197 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from dry heated soil.

NCBI tax id

NCBI tax idMatching level
1120936strain
1990species

strain history

@refhistory
337872002, S. Miyadoh, Kanagawa, Japan: strain SF2197
11270<- S. Miyadoh, SF2197
67770S. Miyadoh SF-2197.
116538CIP <- 2002, S. Miyadoh, Meiji Seika Kaisha Ltd., Kanagawa, Japan: strain SF2197

doi: 10.13145/bacdive16924.20230509.8.1

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 atramentaria
  • full scientific name: Actinomadura atramentaria Miyadoh et al. 1987

@ref: 11270

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura atramentaria

full scientific name: Actinomadura atramentaria Miyadoh et al. 1987 emend. Nouioui et al. 2018

strain designation: SF2197

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.925
69480100positive
116538nopositivefilament-shaped

colony morphology

@refcolony colorincubation periodmedium used
19981Graphite black (9011)10-14 daysISP 2
19981Brown10-14 daysISP 3
19981Brown10-14 daysISP 4
19981Green brown (8000)10-14 daysISP 5
19981Khaki grey (7008)10-14 daysISP 6
19981Khaki grey (7008)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19981yesISP 2
19981yesISP 3Aerial MyceliumSparse/ white
19981yesISP 4Aerial Mycelium
19981yesISP 5Aerial Mycelium
19981noISP 6
19981noISP 7

multimedia

  • @ref: 11270
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43919.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19981ISP 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
19981ISP 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:
19981ISP 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
19981ISP 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
19981ISP 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
19981ISP 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
33787MEDIUM 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)
11270GYM 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
11270ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
116538CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19981positiveoptimum28mesophilic
33787positivegrowth30mesophilic
11270positivegrowth28mesophilic
67770positivegrowth28mesophilic
116538positivegrowth22-41
116538nogrowth5psychrophilic
116538nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116538
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.446

compound production

@refcompound
11270antibiotic SF-2197
19981Matlystatin A
19981Matlystatin B
67770Antibiotic SF-2197

halophily

@refsaltgrowthtested relationconcentration
116538NaClpositivegrowth0-2 %
116538NaClnogrowth4 %
116538NaClnogrowth6 %
116538NaClnogrowth8 %
116538NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1998117234glucose+
1998122599arabinose-
1998117992sucrose-
1998118222xylose-
1998117268myo-inositol-
1998129864mannitol-
1998128757fructose-
1998126546rhamnose+
1998116634raffinose-
1998162968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
1165384853esculin-hydrolysis
11653817632nitrate-reduction
11653816301nitrite-reduction
11653817632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11653835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11653815688acetoin-
11653817234glucose-

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
116538oxidase-
116538beta-galactosidase-3.2.1.23
116538alcohol dehydrogenase-1.1.1.1
116538gelatinase+
116538amylase-
116538DNase-
116538caseinase+3.4.21.50
116538catalase+1.11.1.6
116538tween esterase-
116538gamma-glutamyltransferase-2.3.2.2
116538lecithinase-
116538lipase-
116538lysine decarboxylase-4.1.1.18
116538ornithine decarboxylase-4.1.1.17
116538phenylalanine ammonia-lyase-4.3.1.24
116538protease-
116538tryptophan deaminase-
116538urease-3.5.1.5
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
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
19981-++-+----++----+---
116538+++-+----++---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19981------+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11270dry heated soil
67770Dry-heated soilYaizu City, Shizuoka Pref.JapanJPNAsia
116538Environment, Dry heated soilJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112701Risk group (German classification)
199811German classification
1165381Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura atramentaria 16S rRNA gene, strain DSM 43919TAJ4201381447ena1990
20218Actinomadura atramentaria 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAF134089472ena1990
20218Actinomadura atramentaria 16S rRNA geneU490001409ena1990

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura atramentaria DSM 439191120936.3wgspatric1120936
66792Actinomadura atramentaria DSM 439192519899649draftimg1120936
67770Actinomadura atramentaria DSM 43919 SF2197GCA_000381885scaffoldncbi1120936

GC content

@refGC-contentmethod
6777073.7genome sequence analysis
6777072thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.325no
flagellatedno98.501no
gram-positiveyes91.436no
anaerobicno98.679no
aerobicyes88.937no
halophileno90.557no
spore-formingyes90.077no
thermophileno97.627yes
glucose-utilyes88.945yes
glucose-fermentno92.768no

External links

@ref: 11270

culture collection no.: DSM 43919, IFO 14695, JCM 6250, NBRC 14695, CGMCC 4.2100, CIP 107393, HUT 6547, IMSNU 22157, IMSNU 22161, KCTC 9620, MTCC 2560, NCIMB 12618

straininfo link

  • @ref: 85929
  • straininfo: 50456

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19622664Actinomadura flavalba sp. nov., an endophytic actinomycete isolated from leaves of Maytenus austroyunnanensis.Qin S, Zhao GZ, Li J, Zhu WY, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.010652-02009Actinomycetales/classification/cytology/genetics/*isolation & purification, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Maytenus/*microbiology, Molecular Sequence Data, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Spores, Bacterial/cytologyGenetics
Phylogeny25525125Actinomadura rayongensis sp. nov., isolated from peat swamp forest soil.Phongsopitanun W, Tanasupawat S, Suwanborirux K, Ohkuma M, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.0000332014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Forests, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsGenetics
Genetics27255974Isolation and structure determination of a new lantibiotic cinnamycin B from Actinomadura atramentaria based on genome mining.Kodani S, Komaki H, Ishimura S, Hemmi H, Ohnishi-Kameyama MJ Ind Microbiol Biotechnol10.1007/s10295-016-1788-92016Actinomycetales/*chemistry/genetics/metabolism, Anti-Bacterial Agents/*chemistry/isolation & purification/metabolism/pharmacology, Bacteriocins/biosynthesis/*chemistry/isolation & purification/metabolism/pharmacology, Data Mining, Genome, Bacterial, Genomics, Peptides, Cyclic/chemistryPhylogeny
Phylogeny32845828Actinomadura rubteroloni sp. nov. and Actinomadura macrotermitis sp. nov., isolated from the gut of the fungus growing-termite Macrotermes natalensis.Benndorf R, Martin K, Kufner M, de Beer ZW, Vollmers J, Kaster AK, Beemelmanns CInt J Syst Evol Microbiol10.1099/ijsem.0.0044032020Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gastrointestinal Microbiome, Isoptera/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, South Africa, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11270Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43919)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43919
19981Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43919.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
33787Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4823
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
85929Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50456.1StrainInfo: A central database for resolving microbial strain identifiers
116538Curators of the CIPCollection of Institut Pasteur (CIP 107393)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107393