Strain identifier

BacDive ID: 7982

Type strain: Yes

Species: Micromonospora eburnea

Strain Designation: LK2-10

Strain history: CIP <- 2005, JCM <- 2004, C. Thawai, Chulalongkorn Univ., Bangkok, Thailand: strain LK2-10

NCBI tax ID(s): 227316 (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: 12098

BacDive-ID: 7982

DSM-Number: 44814

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

description: Micromonospora eburnea LK2-10 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 227316
  • Matching level: species

strain history

@refhistory
12098<- Ch. Thawai; LK2-10
67770C. Thawai LK2-10.
118990CIP <- 2005, JCM <- 2004, C. Thawai, Chulalongkorn Univ., Bangkok, Thailand: strain LK2-10

doi: 10.13145/bacdive7982.20230509.8.1

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 eburnea
  • full scientific name: Micromonospora eburnea Thawai et al. 2005

@ref: 12098

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora eburnea

full scientific name: Micromonospora eburnea Thawai et al. 2005

strain designation: LK2-10

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
31287positiveno
69480positive100
118990positivenorod-shaped

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
20126Pastel yellow (1034)10-14 daysISP 2
20126Beige (1001)10-14 daysISP 3
20126Beige (1001)10-14 daysISP 4
20126Beige (1001)10-14 daysISP 5
20126Beige (1001)10-14 daysISP 6
20126Beige (1001)10-14 daysISP 7
1189901

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
20126noISP 2
20126yesISP 3Aerial MyceliumWhite
20126noISP 4
20126noISP 5
20126noISP 6
20126noISP 7

pigmentation

  • @ref: 31287
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12098N-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
12098ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
20126ISP 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
20126ISP 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:
20126ISP 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
20126ISP 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
20126ISP 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
20126ISP 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
36415MEDIUM 375 - for Catellospora koreensisyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.500 g);Agar (15.000 g);Yeast extract (4.000 g);Starch maize (15.000 g);Di Potassium monohydrogenophosphate (0.500 g)
12098CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
12098GPHF-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
118990CIP Medium 375yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=375

culture temp

@refgrowthtypetemperaturerange
20126positiveoptimum28mesophilic
12098positivegrowth28mesophilic
31287positiveoptimum27.5mesophilic
36415positivegrowth25mesophilic
67770positivegrowth28mesophilic
118990positivegrowth25-45
118990nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31287aerobe
118990obligate aerobe

spore formation

@refspore formationconfidence
31287yes
69481yes100
69480yes99.448

halophily

@refsaltgrowthtested relationconcentration
31287NaClpositivegrowth<4 %
118990NaClpositivegrowth0-2 %
118990NaClnogrowth4 %
118990NaClnogrowth6 %
118990NaClnogrowth8 %
118990NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-10(H4), MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2012617234glucose+/-
2012622599arabinose+
2012617992sucrose+/-
2012618222xylose+/-
2012617268myo-inositol+
2012629864mannitol+
2012628757fructose+
2012626546rhamnose+/-
2012616634raffinose+
2012662968cellulose+/-
3128717057cellobiose+carbon source
3128728260galactose+carbon source
3128717234glucose+carbon source
3128717754glycerol+carbon source
3128717716lactose+carbon source
3128729864mannitol+carbon source
3128728053melibiose+carbon source
3128716634raffinose+carbon source
3128726546rhamnose+carbon source
3128717814salicin+carbon source
3128718222xylose+carbon source
3128717632nitrate+reduction
11899016947citrate-carbon source
1189904853esculin+hydrolysis
118990606565hippurate+hydrolysis
11899017632nitrate+reduction
11899016301nitrite-reduction
11899017632nitrate-respiration

metabolite production

  • @ref: 118990
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11899015688acetoin-
11899017234glucose-

enzymes

@refvalueactivityec
31287gelatinase+
118990oxidase-
118990beta-galactosidase-3.2.1.23
118990alcohol dehydrogenase-1.1.1.1
118990gelatinase+
118990amylase+
118990DNase+
118990caseinase+3.4.21.50
118990catalase+1.11.1.6
118990tween esterase+
118990gamma-glutamyltransferase+2.3.2.2
118990lecithinase-
118990lipase-
118990lysine decarboxylase-4.1.1.18
118990ornithine decarboxylase-4.1.1.17
118990phenylalanine ammonia-lyase-4.3.1.24
118990tryptophan deaminase-
118990urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
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
20126-++------+-++-++++-
118990-++++--+-+-++-+++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12098soilYala PrefectureThailandTHAAsia
67770Soil from peat swamp forestLankwai, Yala ProvinceThailandTHAAsia
118990Environment, Soil, forestYalaThailandTHAAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120981Risk group (German classification)
201261German classification
1189901Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12098
  • description: Micromonospora eburnea gene for 16S rRNA, partial sequence, strain:LK2-10
  • accession: AB107231
  • length: 1477
  • database: ena
  • NCBI tax ID: 227316

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora eburnea strain DSM 44814227316.5wgspatric227316
66792Micromonospora eburnea DSM 448142622736604draftimg227316
67770Micromonospora eburnea DSM 44814GCA_900090225contigncbi227316

GC content

@refGC-contentmethod
1209871.5
6777071.5high performance liquid chromatography (HPLC)
6777072.12genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.557yes
gram-positiveyes92.291yes
anaerobicno98.686no
aerobicyes90.434yes
halophileno95.524no
spore-formingyes95.134yes
glucose-utilyes87.352yes
flagellatedno98.377yes
thermophileno95.748yes
glucose-fermentno93.793no

External links

@ref: 12098

culture collection no.: DSM 44814, JCM 12345, PCU 238, TISTR 1531, CIP 108667, NBRC 101912, NRRL B-24761

straininfo link

  • @ref: 77415
  • straininfo: 135124

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653911Micromonospora eburnea sp. nov., isolated from a Thai peat swamp forest.Thawai C, Tanasupawat S, Itoh T, Suwanborirux K, Suzuki KI, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.63217-02005Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Micromonospora/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Thailand, *TreesGenetics
Phylogeny20562246Micromonospora humi sp. nov., isolated from peat swamp forest soil.Songsumanus A, Tanasupawat S, Thawai C, Suwanborirux K, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.024281-02010DNA, Bacterial/genetics, Micromonospora/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Thailand, Trees/microbiologyGenetics
Phylogeny22634700Micromonospora equina sp. nov., isolated from soil from a racecourse.Everest GJ, Meyers PRInt J Syst Evol Microbiol10.1099/ijs.0.042929-02012Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Horses, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, South AfricaGenetics
Phylogeny24108323Micromonospora polyrhachis sp. nov., an actinomycete isolated from edible Chinese black ant (Polyrhachis vicina Roger).Xiang W, Yu C, Liu C, Zhao J, Yang L, Xie B, Li L, Hong K, Wang XInt J Syst Evol Microbiol10.1099/ijs.0.055863-02013Animals, Ants/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics
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
Phylogeny27707427Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.).Ma Z, Zhao S, Cao T, Liu C, Huang Y, Gao Y, Yan K, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0015372016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sonchus/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny30810517Micromonospora caldifontis sp. nov., isolated from hot spring soil.Thawai C, Tanasupawat S, Kudo TInt J Syst Evol Microbiol10.1099/ijsem.0.0033212019Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hot Springs/*microbiology, Micromonospora/*classification/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12098Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44814)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44814
20126Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44814.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
31287Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2760628776041
36415Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6321
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/
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
77415Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135124.1StrainInfo: A central database for resolving microbial strain identifiers
118990Curators of the CIPCollection of Institut Pasteur (CIP 108667)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108667