Strain identifier

BacDive ID: 4258

Type strain: Yes

Species: Dietzia kunjamensis

Strain Designation: K30-10

Strain history: CIP <- 2006, JCM <- 2005, MTCC

NCBI tax ID(s): 322509 (species)

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General

@ref: 12190

BacDive-ID: 4258

DSM-Number: 44907

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, ovoid-shaped

description: Dietzia kunjamensis K30-10 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 322509
  • Matching level: species

strain history

@refhistory
12190<- S. Mayilraj; K30-10
67770S. Mayilraj K30-10.
120510CIP <- 2006, JCM <- 2005, MTCC

doi: 10.13145/bacdive4258.20230509.8.1

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 kunjamensis
  • full scientific name: Dietzia kunjamensis Mayilraj et al. 2006

@ref: 12190

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dietziaceae

genus: Dietzia

species: Dietzia kunjamensis subsp. kunjamensis

full scientific name: Dietzia kunjamensis subsp. kunjamensis (Mayilraj et al. 2006) Nouioui et al. 2018

strain designation: K30-10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31761positive1.1-2.0 µm1-1.2 µmovoid-shapedno
69480no94.87
69480positive100
120510positiveoval-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19887Zinc yellow10-14 daysISP 2
19887Green beige10-14 daysISP 3
19887Pastel orange10-14 daysISP 4
19887Pastel orange10-14 daysISP 5
19887Green beige10-14 daysISP 6
19887Pastel orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19887noISP 2
19887noISP 3
19887noISP 4
19887noISP 5
19887noISP 6
19887noISP 7

pigmentation

  • @ref: 31761
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12190TRYPTICASE 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
19887ISP 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
19887ISP 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:
19887ISP 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
19887ISP 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
19887ISP 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
19887ISP 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
37514MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120510CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116
120510CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19887positiveoptimum30mesophilic
12190positivegrowth30mesophilic
31761positivegrowth20-37
31761positiveoptimum25mesophilic
37514positivegrowth30mesophilic
60412positivegrowth30-37mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31761positivegrowth07-10alkaliphile
31761positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31761aerobe
60412aerobe
120510obligate aerobe

spore formation

@refspore formationconfidence
31761no
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
31761NaClpositivegrowth0-5 %
31761NaClpositiveoptimum0-5 %

observation

@refobservation
31761aggregates in chains
67770quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3176122599arabinose+carbon source
3176123652dextrin+carbon source
3176133984fucose+carbon source
3176128260galactose+carbon source
3176129987glutamate+carbon source
3176117754glycerol+carbon source
3176127082trehalose+carbon source
3176118222xylose+carbon source
12051017632nitrate+reduction
12051016301nitrite-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: 120510
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31761catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
120510oxidase-
120510catalase+1.11.1.6
120510urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19887-+-+--+-++-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19887+++-++--+++-+-++-+-
120510+++-+-++-++---+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12190soilcold desert of the HimalayasIndiaINDAsia
60412Soilcold soil of the HimalayasIndiaINDAsia
67770SoilKunjam Pass, the Indian HimalayasIndiaINDAsia
120510Environment, Soil sample, cold desertIndian HimalayasIndiaINDAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4509.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_611;97_2732;98_3390;99_4509&stattab=map
  • Last taxonomy: Dietzia
  • 16S sequence: FJ468332
  • Sequence Identity:
  • Total samples: 11008
  • soil counts: 1292
  • aquatic counts: 2957
  • animal counts: 6479
  • plant counts: 280

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121901Risk group (German classification)
198871Risk group (German classification)
1205101Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Dietzia kunjamensis strain DSM 44907 16S ribosomal RNA gene, partial sequenceFJ4683321439ena322509
12190Dietzia kunjamensis strain K30-10 16S ribosomal RNA gene, partial sequenceAY9724801455ena322509

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dietzia kunjamensis strain DSM 44907322509.3wgspatric322509
66792Dietzia kunjamensis DSM 449072728369259draftimg322509
67770Dietzia kunjamensis DSM 44907GCA_003610395contigncbi322509

GC content

@refGC-contentmethod
3176167
6777067thermal denaturation, midpoint method (Tm)
6777070.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno64no
gram-positiveyes90.184no
anaerobicno98.887no
halophileno52.712no
spore-formingno87.471no
glucose-utilyes85.629no
motileno94.859yes
flagellatedno98.528no
aerobicyes87.748no
thermophileno98.389yes
glucose-fermentno86.933yes

External links

@ref: 12190

culture collection no.: DSM 44907, JCM 13325, MTCC 7007, CCUG 54952, BCRC 16834, CIP 109330, NBRC 105042, NCIMB 14304

straininfo link

  • @ref: 73753
  • straininfo: 297170

literature

  • topic: Phylogeny
  • Pubmed-ID: 16825647
  • title: Dietzia kunjamensis sp. nov., isolated from the Indian Himalayas.
  • authors: Mayilraj S, Suresh K, Kroppenstedt RM, Saini HS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64212-0
  • year: 2006
  • mesh: Actinomycetales/*classification/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12190Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44907)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44907
19887Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44907.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
31761Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128034
37514Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7060
60412Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54952)https://www.ccug.se/strain?id=54952
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
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)
73753Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297170.1StrainInfo: A central database for resolving microbial strain identifiers
120510Curators of the CIPCollection of Institut Pasteur (CIP 109330)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109330