Strain identifier

BacDive ID: 7990

Type strain: Yes

Species: Micromonospora echinaurantiaca

Strain Designation: 65-m50

Strain history: CIP <- 2005, DSMZ <- JCM <- KCC <- X. Yan: strain 65-m50

NCBI tax ID(s): 47857 (species)

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General

@ref: 11379

BacDive-ID: 7990

DSM-Number: 43904

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

description: Micromonospora echinaurantiaca 65-m50 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 47857
  • Matching level: species

strain history

@refhistory
11379<- JCM (Micromonospora echinoaurantiaca) <- KCC <- X. Yan, 65-m50
67770KCC A-0257 <-- X. Yan 65-m50.
118994CIP <- 2005, DSMZ <- JCM <- KCC <- X. Yan: strain 65-m50

doi: 10.13145/bacdive7990.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Micromonospora
  • species: Micromonospora echinaurantiaca
  • full scientific name: Micromonospora echinaurantiaca Kroppenstedt et al. 2005

@ref: 11379

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora echinaurantiaca

full scientific name: Micromonospora echinaurantiaca Kroppenstedt et al. 2005

strain designation: 65-m50

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
118994positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19614Signal orange10-14 daysISP 2
19614Deep orange10-14 daysISP 3
19614Signal orange10-14 daysISP 4
19614Pastel yellow10-14 daysISP 5
19614Signal orange10-14 daysISP 6
19614Pastel yellow10-14 daysISP 7
118994

multicellular morphology

@refforms multicellular complexmedium name
19614noISP 2
19614noISP 3
19614noISP 4
19614noISP 5
19614noISP 6
19614noISP 7

multimedia

  • @ref: 11379
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43904.jpg
  • caption: Medium 554 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11379N-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
11379GYM 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
19614ISP 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
19614ISP 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:
19614ISP 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
19614ISP 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
19614ISP 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
19614ISP 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
36424MEDIUM 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)
118994CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11379positivegrowth28mesophilic
36424positivegrowth25mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118994
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.999

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1961417234glucose+
1961422599arabinose+
1961417992sucrose+
1961418222xylose-
1961417268myo-inositol-
1961429864mannitol+
1961428757fructose+
1961426546rhamnose-
1961416634raffinose+
1961462968cellulose+
11899417632nitrate+reduction
11899416301nitrite-reduction

metabolite production

  • @ref: 118994
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118994oxidase-
118994alcohol dehydrogenase-1.1.1.1
118994catalase+1.11.1.6
118994lysine decarboxylase-4.1.1.18
118994ornithine decarboxylase-4.1.1.17
118994urease-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
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
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
19614+++-++-+-++++-+-+--
118994+++-++-+-++-+-+-+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11379soil
67770SoilBeijingChinaCHNAsia
118994Environment, SoilChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113791Risk group (German classification)
196141Risk group (German classification)
1189941Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11379
  • description: Micromonospora echinaurantiaca 16S rRNA gene, type strain DSM 43904
  • accession: X92618
  • length: 1474
  • database: ena
  • NCBI tax ID: 47857

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora echinaurantiaca DSM 43904GCA_900090235chromosomencbi47857
66792Micromonospora echinaurantiaca strain DSM 4390447857.4completepatric47857
66792Micromonospora echinaurantiaca DSM 439042623620557draftimg47857

GC content

  • @ref: 67770
  • GC-content: 73.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.925no
anaerobicno99.373no
halophileno93.098no
spore-formingyes93.134no
glucose-utilyes88.235yes
aerobicyes96.054no
thermophileno98.7yes
flagellatedno97.293no
motileno93.684no
glucose-fermentno93.022no

External links

@ref: 11379

culture collection no.: DSM 43904, ATCC 35572, CIP 108948, IFO 14022, JCM 3257, KCC A-0257, NBRC 14022, NRRL B-16102, BCRC 13324, CGMCC 4.1254, IMSNU 21290

straininfo link

  • @ref: 77420
  • straininfo: 45996

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15997706Eight new species of the genus Micromonospora, Micromonospora citrea sp. nov., Micromonospora echinaurantiaca sp. nov., Micromonospora echinofusca sp. nov. Micromonospora fulviviridis sp. nov., Micromonospora inyonensis sp. nov., Micromonospora peucetia sp. nov., Micromonospora sagamiensis sp. nov., and Micromonospora viridifaciens sp. nov.Kroppenstedt RM, Mayilraj S, Wink JM, Kallow W, Schumann P, Secondini C, Stackebrandt ESyst Appl Microbiol10.1016/j.syapm.2004.12.0112005Carbohydrates/analysis, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Isomerism, Micromonospora/*classification/cytology/genetics/physiology, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Ribotyping, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Vitamin K 2/analysis
Phylogeny26358439Micromonospora fluostatini sp. nov., isolated from marine sediment.Phongsopitanun W, Kudo T, Mori M, Shiomi K, Pittayakhajonwut P, Suwanborirux K, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0005892015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Thailand, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11379Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43904)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43904
19614Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43904.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
36424Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6634
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
77420Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45996.1StrainInfo: A central database for resolving microbial strain identifiers
118994Curators of the CIPCollection of Institut Pasteur (CIP 108948)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108948