Strain identifier

BacDive ID: 16965

Type strain: Yes

Species: Thermomonospora echinospora

Strain Designation: Mb3-1, Mb3-1

Strain history: KCC A-0148 <-- H. Nonomura Mb3-1.

NCBI tax ID(s): 1992 (species)

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General

@ref: 10831

BacDive-ID: 16965

DSM-Number: 43163

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Thermomonospora echinospora Mb3-1 is a mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 1992
  • Matching level: species

strain history

@refhistory
10831<- KCC <- H. Nonomura, FYU, Mb3-1
67770KCC A-0148 <-- H. Nonomura Mb3-1.

doi: 10.13145/bacdive16965.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Thermomonospora
  • species: Thermomonospora echinospora
  • full scientific name: Thermomonospora echinospora (Nonomura and Ohara 1971) Nouioui et al. 2018

  • synonyms

    @refsynonym
    20215Microbispora echinospora
    20215Actinomadura echinospora

@ref: 10831

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Thermomonospora

species: Thermomonospora echinospora

full scientific name: Thermomonospora echinospora (Nonomura and Ohara 1971) Nouioui et al. 2018

strain designation: Mb3-1, Mb3-1

type strain: yes

Morphology

colony morphology

@refincubation periodmedium usedcolony color
1955110-14 daysISP 2
1955110-14 daysISP 3
1955110-14 daysISP 4Ochre brown
1955110-14 daysISP 5Ochre brown
1955110-14 daysISP 6
1955110-14 daysISP 7Ochre brown

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19551noISP 2
19551noISP 3
19551yesISP 4Aerial Mycelium
19551yesISP 5Aerial MyceliumWhite
19551noISP 6
19551yesISP 7Aerial MyceliumWhite

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10831GYM 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
19551ISP 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
19551ISP 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:
19551ISP 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
19551ISP 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
19551ISP 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
19551ISP 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
10831ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19551positiveoptimum37mesophilic
10831positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

halophily

  • @ref: 19551
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19551-----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
10831soilJapanJPNAsia
67770SoilJapanJPNAsiaYamanashi Pref.

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
108311Risk group (German classification)
195511Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura echinospora strain ATCC27300 16S ribosomal RNA gene, partial sequenceAF051389195ena1992
20218Actinomadura echinospora 16S rRNA gene, strain DSM 43163TAJ4201351440ena1992
20218Actinomadura echinospora 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAF134095457ena1992
20218Actinomadura echinospora 16S rRNA geneU490041401ena1992

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura echinospora strain DSM 431631992.4wgspatric1992
66792Thermomonospora echinospora DSM 431632634166348draftimg1992
67770Thermomonospora echinospora DSM 43163GCA_900108175scaffoldncbi1992

GC content

@refGC-contentmethod
6777067thermal denaturation, midpoint method (Tm)
6777071.8genome sequence analysis
6777074thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.745no
gram-positiveyes86.782no
anaerobicno98.083no
aerobicyes87.104no
halophileno94.479no
spore-formingyes86.764no
glucose-utilyes88.733no
flagellatedno97.563no
thermophileno95.065yes
glucose-fermentno90.894no

External links

@ref: 10831

culture collection no.: DSM 43163, ATCC 27300, IFO 14042, JCM 3148, NBRC 14042, BCRC 12547, CBS 263.72, HUT 6548, IMSNU 22163, KCTC 9313, MTCC 1544

straininfo link

  • @ref: 85969
  • straininfo: 297054

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2283505A taxonomic review of the genus Microbispora and a proposal to transfer two species to the genus Actinomadura and to combine ten species into Microbispora rosea.Miyadoh S, Amano S, Tohyama H, Shomura TJ Gen Microbiol10.1099/00221287-136-9-19051990Actinomycetales/*classification/genetics/ultrastructure, DNA, Bacterial/analysis, Fatty Acids/analysis, Microscopy, Electron, Scanning, Spores, Bacterial/ultrastructure
Phylogeny25944084Actinomadura amylolytica sp. nov. and Actinomadura cellulosilytica sp. nov., isolated from geothermally heated soil.Jiao JY, Liu L, Zhou EM, Wei DQ, Ming H, Xian WD, Yuan CG, Zhong JM, Li WJAntonie Van Leeuwenhoek10.1007/s10482-015-0465-82015Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Geothermal Energy, Hot Temperature, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytologyStress
Phylogeny30777821Actinomadura craniellae sp. nov., isolated from a marine sponge in the South China Sea.Li L, Xu QH, Wang XT, Lin HW, Lu YHInt J Syst Evol Microbiol10.1099/ijsem.0.0032952019Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10831Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43163)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43163
19551Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43163.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
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/
68368Automatically annotated from API 20E
85969Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297054.1StrainInfo: A central database for resolving microbial strain identifiers