Strain identifier

BacDive ID: 16989

Type strain: Yes

Species: Actinomadura meyerae

Strain Designation: A288

Strain history: CIP <- 2004, DSMZ <- E.T. Quintana, UK: strain A288 <- M.E. Trujillo

NCBI tax ID(s): 240840 (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: 12034

BacDive-ID: 16989

DSM-Number: 44715

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

description: Actinomadura meyerae A288 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 240840
  • Matching level: species

strain history

@refhistory
12034<- E. T. Quintana; A288 <- M. E. Trujillo
67770DSM 44715 <-- A. Quintana A288 <-- M. E. Trujillo.
120932CIP <- 2004, DSMZ <- E.T. Quintana, UK: strain A288 <- M.E. Trujillo

doi: 10.13145/bacdive16989.20230509.8.1

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 meyerae
  • full scientific name: Actinomadura meyerae corrig. Quintana et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Actinomadura meyerii

@ref: 12034

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura meyerae

full scientific name: Actinomadura meyerae Quintana et al. 2004 emend. Nouioui et al. 2018

strain designation: A288

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480positive100
120932positiveno

colony morphology

@refcolony colorincubation periodmedium used
19694Beige10-14 daysISP 2
19694Beige10-14 daysISP 3
19694Beige10-14 daysISP 4
1969410-14 daysISP 5
19694Beige10-14 daysISP 6
19694Beige10-14 daysISP 7
120932

multicellular morphology

@refforms multicellular complexmedium name
19694noISP 2
19694noISP 3
19694noISP 4
19694noISP 5
19694noISP 6
19694noISP 7

multimedia

  • @ref: 12034
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44715.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12034GPHF-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
12034GYM 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
19694ISP 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
19694ISP 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:
19694ISP 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
19694ISP 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
19694ISP 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
19694ISP 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
33963MEDIUM 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)
120932CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
12034positivegrowth28mesophilic
19694positiveoptimum28mesophilic
33963positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120932
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12093217632nitrate+reduction
12093216301nitrite-reduction
12093217632nitrate-respiration

enzymes

@refvalueactivityec
120932oxidase+
120932alcohol dehydrogenase-1.1.1.1
120932catalase+1.11.1.6
120932lysine decarboxylase-4.1.1.18
120932ornithine decarboxylase-4.1.1.17
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
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
19694+++-++---++---++---
120932+++-++-+-++---+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12034garden soilMexico CityMexicoMEXNorth America
67770Garden soilMexico CityMexicoMEXNorth America
120932Environment, Garden soilMexicoMEXNorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120341Risk group (German classification)
1209321Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12034
  • description: Actinomadura meyerii A288 16S ribosomal RNA gene, partial sequence
  • accession: AY273787
  • length: 1480
  • database: ena
  • NCBI tax ID: 240840

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura meyerae strain DSM 44715240840.3wgspatric240840
66792Actinomadura meyerae DSM 447152700988714draftimg240840
67770Actinomadura meyerae DSM 44715GCA_900188445scaffoldncbi240840

GC content

  • @ref: 67770
  • GC-content: 72.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.438no
gram-positiveyes90.68no
anaerobicno98.389no
aerobicyes87.106no
halophileno86.767no
spore-formingyes93.391no
glucose-utilyes86.948no
flagellatedno98.29no
thermophileno92.793no
glucose-fermentno91.024no

External links

@ref: 12034

culture collection no.: DSM 44715, NRRL B-24247, JCM 13237, CIP 108410

straininfo link

  • @ref: 85992
  • straininfo: 131406

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22021584Actinomadura geliboluensis sp. nov., isolated from soil.Sazak A, Camas M, Sproer C, Klenk HP, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.036145-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Carbohydrates/analysis, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, TurkeyGenetics
Phylogeny22523172Actinomadura xylanilytica sp. nov., an actinomycete isolated from soil.Zucchi TD, Kim BY, Bonda ANV, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.042325-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Carbohydrates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12034Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44715)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44715
19694Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44715.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
33963Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6030
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/
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
85992Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131406.1StrainInfo: A central database for resolving microbial strain identifiers
120932Curators of the CIPCollection of Institut Pasteur (CIP 108410)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108410