Strain identifier

BacDive ID: 8008

Type strain: Yes

Species: Micromonospora tulbaghiae

Strain Designation: TVU1

Strain history: DSM 45142 <-- P. R. Meyers TVU1 <-- B. M. Kirby.

NCBI tax ID(s): 479978 (species)

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General

@ref: 12386

BacDive-ID: 8008

DSM-Number: 45142

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

description: Micromonospora tulbaghiae TVU1 is a spore-forming, Gram-positive bacterium that was isolated from leaves of wild garlic, Tulbaghia violacea.

NCBI tax id

  • NCBI tax id: 479978
  • Matching level: species

strain history

@refhistory
12386<- P. R. Meyers, Univ. Cape Town, South Africa; TVU1 <- B. M. Kirby
67770DSM 45142 <-- P. R. Meyers TVU1 <-- B. M. Kirby.

doi: 10.13145/bacdive8008.20240916.9.1

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 tulbaghiae
  • full scientific name: Micromonospora tulbaghiae Kirby and Meyers 2010

@ref: 12386

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora tulbaghiae

full scientific name: Micromonospora tulbaghiae Kirby and Meyers 2010

strain designation: TVU1

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
29444positive
69480positive92.823

colony morphology

@refcolony colorincubation periodmedium used
21386Olive brown (8008)10-14 daysISP 2
21386Orange brown (8023)10-14 daysISP 3
21386Yellow orange (2000)10-14 daysISP 4
21386Yellow Orange (2000)10-14 daysISP 5
21386Ochre brown (8001)10-14 daysISP 7
21386Daffodil yellow (1007)10-14 daysSuter with tyrosine
21386Saffran yellow (1017)10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21386noISP 2
21386noISP 3
21386noISP 4
21386noISP 5
21386noISP 7
21386noSuter with tyrosine
21386noSuter without tyrosine

pigmentation

  • @ref: 29444
  • production: no

multimedia

  • @ref: 12386
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45142.jpg
  • caption: Medium 554 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12386N-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
21386ISP 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
21386ISP 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:
21386ISP 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
21386ISP 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
21386ISP 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
21386Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21386Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
12386TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
12386GYM 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

culture temp

@refgrowthtypetemperature
12386positivegrowth28
29444positivegrowth04-37
67770positivegrowth28

culture pH

  • @ref: 29444
  • ability: positive
  • type: growth
  • pH: 07-09
  • PH range: alkaliphile

Physiology and metabolism

spore formation

@refspore formationconfidence
29444yes
69480yes92.814

halophily

@refsaltgrowthtested relationconcentration
21386NaClpositivemaximum5 %
29444NaClpositivegrowth5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2138617234glucose+
2138622599arabinose+
2138617992sucrose+
2138618222xylose+
2138617268myo-inositol+
2138637684mannose+
2138628757fructose+
2138626546rhamnose+
2138616634raffinose+
2138662968cellulose+
2944428757fructose+carbon source
2944417234glucose+carbon source
2944429864mannitol+carbon source
2944417268myo-inositol+carbon source
2944426546rhamnose+carbon source
2944433942ribose+carbon source
6837917632nitrate-reduction
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 29444
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
29444gelatinase+
68379gelatinase+
68379urease-3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
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-
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-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACGLYG
21386-------+/--+-------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21386-++-+++++--++-+-+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
12386leaves of wild garlic, Tulbaghia violaceaTulbaghia violaceaCape Town, WellingtonSouth AfricaZAFAfrica
67770Leaves of wild garlic, Tulbaghia violaceaTulbaghia violacea

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

Safety information

risk assessment

  • @ref: 12386
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12386
  • description: Micromonospora tulbaghiae strain TVU1 16S ribosomal RNA gene, partial sequence
  • accession: EU196562
  • length: 1435
  • database: nuccore
  • NCBI tax ID: 479978

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora tulbaghiae strain DSM 45142479978.4wgspatric479978
66792Micromonospora tulbaghiae DSM 451422622736612draftimg479978
67770Micromonospora tulbaghiae DSM 45142GCA_900091605scaffoldncbi479978

GC content

  • @ref: 67770
  • GC-content: 72.95
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes92.823yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.396no
69480spore-formingspore-formingAbility to form endo- or exosporesyes92.814no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.598no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno89.5no

External links

@ref: 12386

culture collection no.: DSM 45142, JCM 18297, NRRL B-24576

straininfo link

  • @ref: 77438
  • straininfo: 399689

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19667372Micromonospora tulbaghiae sp. nov., isolated from the leaves of wild garlic, Tulbaghia violacea.Kirby BM, Meyers PRInt J Syst Evol Microbiol10.1099/ijs.0.013243-02009DNA Gyrase/genetics, DNA, Bacterial/genetics/isolation & purification, Garlic/*microbiology, Micromonospora/classification/genetics/growth & development/*isolation & purification, Molecular Sequence Data, Peas/microbiology, Phylogeny, Plant Leaves/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsEnzymology
Metabolism29974366Actinoplanes deserti sp. nov., isolated from a desert soil sample.Habib N, Khan IU, Chu X, Xiao M, Li S, Fang BZ, Zhi XY, Li WJAntonie Van Leeuwenhoek10.1007/s10482-018-1121-x2018Base Composition, Cell Wall/*chemistry/metabolism, China, Desert Climate, Diaminopimelic Acid/metabolism, Fatty Acids/metabolism, Galactose/metabolism, Glucose/metabolism, Glycolipids/metabolism, Mannose/metabolism, Micromonosporaceae/classification/*genetics/isolation & purification, Peptidoglycan/*chemistry/metabolism, Phospholipids/metabolism, *Phylogeny, RNA, Ribosomal, 16S/*genetics, Ribose/metabolism, Soil Microbiology, Spores, Bacterial/chemistry/growth & development, Vitamin K 2/metabolism, Xylose/metabolismPhylogeny
Phylogeny33174828Micromonospora fluminis sp. nov., isolated from mountain river sediment.Camacho Pozo MI, Wieme AD, Rodriguez Perez S, Llaurado Maury G, Peeters C, Snauwaert C, Lescaylle Veranes Y, Pena Zamora L, Schumann P, Vandamme PAInt J Syst Evol Microbiol10.1099/ijsem.0.0045542020Bacterial Typing Techniques, Base Composition, Cuba, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Micromonospora/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12386Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45142)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45142
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
21386Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45142.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29444Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2585028776041
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/
68379Automatically annotated from API Coryne
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)
77438Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399689.1StrainInfo: A central database for resolving microbial strain identifiers