Strain identifier

BacDive ID: 4263

Type strain: Yes

Species: Dietzia timorensis

Strain Designation: ID05-A0528

Strain history: DSM 45568 <-- NBRC 104184 <-- K. Ando and Y. Widyastuti ID05-A0528.

NCBI tax ID(s): 499555 (species)

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General

@ref: 17660

BacDive-ID: 4263

DSM-Number: 45568

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped, human pathogen

description: Dietzia timorensis ID05-A0528 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from soil.

NCBI tax id

  • NCBI tax id: 499555
  • Matching level: species

strain history

@refhistory
17660<- NBRC <- K. Ando (NITE) and Y. Widyastuti(LIPI); ID05-A0528
67770DSM 45568 <-- NBRC 104184 <-- K. Ando and Y. Widyastuti ID05-A0528.

doi: 10.13145/bacdive4263.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Dietziaceae
  • genus: Dietzia
  • species: Dietzia timorensis
  • full scientific name: Dietzia timorensis Yamamura et al. 2010

@ref: 17660

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dietziaceae

genus: Dietzia

species: Dietzia timorensis

full scientific name: Dietzia timorensis Yamamura et al. 2010

strain designation: ID05-A0528

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29394positiverod-shapedno
69480no93.377
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21435Golden yellow10-14 daysISP 2
21435Sand yellow (1002)10-14 daysISP 5
21435Light ivory (1015)10-14 daysISP 7
21435Sand yellow (1002)10-14 daysSuter with tyrosine
21435Light ivory (1015)10-14 daysSuter without tyrosine

pigmentation

  • @ref: 29394
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17660TRYPTICASE 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
21435ISP 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
21435ISP 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
21435ISP 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
21435Suter 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
21435Suter 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

culture temp

@refgrowthtypetemperaturerange
17660positivegrowth28mesophilic
29394positivegrowth10-37
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 29394
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.979

halophily

@refsaltgrowthtested relationconcentration
21435NaClpositivemaximum10 %
29394NaClpositivegrowth0-7 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2143517234glucose+
2143522599arabinose-
2143517992sucrose-
2143518222xylose-
2143517268myo-inositol-
2143537684mannose-
2143528757fructose+
2143526546rhamnose-
2143516634raffinose-
2143562968cellulose-
2939415963ribitol+carbon source
2939422599arabinose+carbon source
2939418403L-arabitol+carbon source
2939417057cellobiose+carbon source
2939428757fructose+carbon source
2939433984fucose+carbon source
2939428260galactose+carbon source
2939417234glucose+carbon source
2939417754glycerol+carbon source
2939428087glycogen+carbon source
2939417716lactose+carbon source
2939417306maltose+carbon source
2939429864mannitol+carbon source
2939437684mannose+carbon source
2939428053melibiose+carbon source
29394506227N-acetylglucosamine+carbon source
2939416634raffinose+carbon source
2939426546rhamnose+carbon source
2939433942ribose+carbon source
2939417814salicin+carbon source
2939430911sorbitol+carbon source
2939417992sucrose+carbon source
2939427082trehalose+carbon source
2939417151xylitol+carbon source
2939418222xylose+carbon source
293944853esculin+hydrolysis
6836925115malate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382lipase (C 14)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
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
68379pyrazinamidase-3.5.1.B15
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21435---+--+------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
21435++/-++++/-++/--++/----++---
17660++/-+/-+-----++---++----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
17660-----+/---++/-++++/-+-+/-+++/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
17660soilKupang, West TimorIndonesiaIDNAsia
67770Soil under mahogany (Swietenia mahogani) treesWest TimorIndonesiaIDNAsiaSwietenia mahogani

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3618.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_611;97_2256;98_2769;99_3618&stattab=map
  • Last taxonomy: Dietzia timorensis subclade
  • 16S sequence: AB377289
  • Sequence Identity:
  • Total samples: 5699
  • soil counts: 785
  • aquatic counts: 1266
  • animal counts: 3554
  • plant counts: 94

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
17660yes, in single cases1Risk group (German classification)
21435L1German classification

Sequence information

16S sequences

  • @ref: 17660
  • description: Dietzia timorensis gene for 16S ribosomal RNA, partial sequence, strain: ID05-A0528
  • accession: AB377289
  • length: 1455
  • database: ena
  • NCBI tax ID: 499555

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dietzia timorensis ID05-A0528GCA_001659785completencbi499555
66792Dietzia timorensis ID05-A05282744054500draftimg499555
67770Dietzia timorensis ID05-A0528GCA_001651825scaffoldncbi499555

GC content

@refGC-contentmethod
1766065.5
6777065.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
flagellatedno97.686yes
gram-positiveyes88.291yes
anaerobicno99.143no
aerobicyes89.513yes
halophileyes54.588no
spore-formingno87.66no
glucose-utilyes85.216yes
motileno93.972yes
thermophileno98.103yes
glucose-fermentno86.192yes

External links

@ref: 17660

culture collection no.: DSM 45568, BTCC B-560, JCM 18295, NBRC 104184

straininfo link

  • @ref: 73758
  • straininfo: 405815

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19654365Dietzia timorensis sp. nov., isolated from soil.Yamamura H, Lisdiyanti P, Ridwan R, Ratnakomala S, Sarawati R, Lestari Y, Triana E, Kartina G, Widyastuti Y, Ando KInt J Syst Evol Microbiol10.1099/ijs.0.012229-02009Actinomycetales/*classification/genetics/isolation & purification, Base Sequence, Indonesia, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny27130323Lawsonella clevelandensis gen. nov., sp. nov., a new member of the suborder Corynebacterineae isolated from human abscesses.Bell ME, Bernard KA, Harrington SM, Patel NB, Tucker TA, Metcalfe MG, McQuiston JRInt J Syst Evol Microbiol10.1099/ijsem.0.0011222016Abscess/*microbiology, Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Humans, Male, Middle Aged, Muramic Acids/chemistry, Mycolic Acids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spine/microbiology/pathologyPathogenicity
Genetics27765661The complete genome of Dietzia timorensis ID05-A0528(T) revealed the genetic basis for its saline-alkali tolerance.Fang H, Hu B, Nie Y, Tang YQ, Wu XLJ Biotechnol10.1016/j.jbiotec.2016.10.0152016Actinomycetales/*genetics/*physiology, DNA, Bacterial/analysis/genetics, Genome, Bacterial/*genetics, Petroleum, Salt Tolerance/*genetics, Sequence Analysis, DNA, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17660Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45568)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45568
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
21435Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45568.pdfCompendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig
29394Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2580128776041
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/
68369Automatically annotated from API 20NE
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
73758Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405815.1StrainInfo: A central database for resolving microbial strain identifiers