Strain identifier

BacDive ID: 4265

Type strain: Yes

Species: Dietzia alimentaria

Strain Designation: 72

Strain history: J.-W. Bae 72.

NCBI tax ID(s): 1077144 (strain), 665550 (species)

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General

@ref: 18108

BacDive-ID: 4265

DSM-Number: 45698

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

description: Dietzia alimentaria 72 is a mesophilic bacterium that was isolated from traditional salt-fermented seafood made of clam jeotgal.

NCBI tax id

NCBI tax idMatching level
665550species
1077144strain

strain history

@refhistory
18108<- S. W. Kwon, KACC; KACC 21126
67770J.-W. Bae 72.

doi: 10.13145/bacdive4265.20230509.8.1

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 alimentaria
  • full scientific name: Dietzia alimentaria Kim et al. 2011

@ref: 18108

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dietziaceae

genus: Dietzia

species: Dietzia alimentaria

full scientific name: Dietzia alimentaria Kim et al. 2011 emend. Nouioui et al. 2018

strain designation: 72

type strain: yes

Morphology

colony morphology

@refincubation periodcolony colormedium used
181083-7 days
2143910-14 daysBright red orange (2008)ISP 2
2143910-14 daysPastel yellow (1034)ISP 5
2143910-14 daysPastel yellow (1034)ISP 6
2143910-14 daysPastel yellow (1034)ISP 7
2143910-14 daysLight ivory (1015)Suter with tyrosine
2143910-14 daysSalmon orange (2012)Suter without tyrosine

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18108GYM 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
21439ISP 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
21439ISP 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
21439ISP 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
21439ISP 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
21439Suter 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
21439Suter 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
18108positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

halophily

  • @ref: 21439
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2143917234glucose+
2143922599arabinose-
2143917992sucrose-
2143918222xylose-
2143917268myo-inositol-
2143937684mannose-
2143928757fructose-
2143926546rhamnose-
2143916634raffinose-
2143962968cellulose-
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

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
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21439---+-------------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21439++/-+/-+++/-+/---++/---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18108traditional salt-fermented seafood made of clam jeotgalSokchoRepublic of KoreaKORAsia
67770Traditional salt-fermented seafood made of clam jeotgalSokcho, Gangwon-do ProvinceRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Seafood
#Engineered#Food production#Fermented

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
181081Risk group (German classification)
21439L1German classification

Sequence information

16S sequences

  • @ref: 18108
  • description: Dietzia alimentaria 72 16S ribosomal RNA gene, partial sequence
  • accession: GQ368824
  • length: 1439
  • database: ena
  • NCBI tax ID: 1077144

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dietzia alimentaria 721077144.3wgspatric1077144
66792Dietzia alimentaria 722547132114draftimg1077144
67770Dietzia alimentaria 72GCA_000226215contigncbi1077144

GC content

@refGC-contentmethod
1810864.7
6777067.34genome sequence analysis
6777064.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.321no
flagellatedno98.93no
gram-positiveyes91no
anaerobicno98.743no
aerobicyes86.042no
halophileno62.438no
spore-formingno83.219no
thermophileno97.952no
glucose-utilyes87.108yes
glucose-fermentno89.609yes

External links

@ref: 18108

culture collection no.: DSM 45698, JCM 16360, KACC 21126, NBRC 109780

straininfo link

  • @ref: 73760
  • straininfo: 407168

literature

  • topic: Phylogeny
  • Pubmed-ID: 20952550
  • title: Dietzia alimentaria sp. nov., isolated from a traditional Korean food.
  • authors: Kim J, Roh SW, Choi JH, Jung MJ, Nam YD, Kim MS, Park EJ, Shin KS, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.021501-0
  • year: 2010
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, *Food Microbiology, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature
  • topic2: Biotechnology

Reference

@idauthorscataloguedoi/urltitle
18108Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45698)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45698
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
21439Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45698.pdfCompendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
73760Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407168.1StrainInfo: A central database for resolving microbial strain identifiers