Strain identifier

BacDive ID: 24246

Type strain: Yes

Species: Kribbella shirazensis

Strain history: <- J. Hamedi, Univ. Tehran, Iran <- F. Mohammadipanah; UTMC 693

NCBI tax ID(s): 1105143 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 20623

BacDive-ID: 24246

DSM-Number: 45490

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Kribbella shirazensis DSM 45490 is an aerobe, spore-forming, mesophilic bacterium that was isolated from non-rhizosphere clay soil.

NCBI tax id

  • NCBI tax id: 1105143
  • Matching level: species

strain history

  • @ref: 20623
  • history: <- J. Hamedi, Univ. Tehran, Iran <- F. Mohammadipanah; UTMC 693

doi: 10.13145/bacdive24246.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Kribbellaceae
  • genus: Kribbella
  • species: Kribbella shirazensis
  • full scientific name: Kribbella shirazensis Mohammadipanah et al. 2013

@ref: 20623

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kribbellaceae

genus: Kribbella

species: Kribbella shirazensis

full scientific name: Kribbella shirazensis Mohammadipanah et al. 2013

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30886positiverod-shapedno
69480positive100

colony morphology

@refincubation periodmedium usedcolony color
2143210-14 daysISP 2
2143210-14 daysISP 3
2143210-14 daysISP 4Ivory (1014)
2143210-14 daysISP 5Light ivory (1015)
2143210-14 daysISP 6Light ivory (1015)
2143210-14 daysISP 7Light ivory (1015)
2143210-14 daysSuter with tyrosineIvory (1014)
2143210-14 daysSuter without tyrosineLight ivory (1015)
627102 days

pigmentation

  • @ref: 30886
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
20623https://www.dsmz.de/microorganisms/photos/DSM_45490.jpgMedium 65 28°C© Leibniz-Institut DSMZ
66793EM_DSM_45490_1.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20623BHI MEDIUM (DSMZ Medium 215)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium215.pdf
20623TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
20623R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
20623GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
21432ISP 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
21432ISP 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:
21432ISP 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
21432ISP 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
21432ISP 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
21432ISP 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
21432Suter 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
21432Suter 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
20623GYM 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

@refgrowthtypetemperaturerange
20623positivegrowth28mesophilic
30886positiveoptimum28mesophilic
62710positivegrowth37mesophilic

culture pH

  • @ref: 30886
  • ability: positive
  • type: optimum
  • pH: 7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30886aerobe
62710aerobe

spore formation

@refspore formationconfidence
30886yes
69481yes100
69480yes98.853

halophily

@refsaltgrowthtested relationconcentration
21432NaClpositivemaximum7.5 %
30886NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2143217234glucose+
2143222599arabinose+
2143217992sucrose+
2143218222xylose+
2143217268myo-inositol+
2143237684mannose+
2143228757fructose+
2143226546rhamnose+
2143216634raffinose+
2143262968cellulose-
3088617057cellobiose+carbon source
3088628757fructose+carbon source
3088625115malate+carbon source
3088617306maltose+carbon source
30886506227N-acetylglucosamine+carbon source
3088617992sucrose+carbon source
3088627082trehalose+carbon source
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

enzymes

@refvalueactivityec
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
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
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

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21432-+++-+++++++/---+/-+/--++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21432+++/--++++-++/-+/-+-+++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
20623non-rhizosphere clay soilFars Province, ShirazIranIRNAsia
62710Soil,rhizosphericalShiraz,FarsIranIRNAsia2008

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_71347.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_440;97_503;98_16379;99_71347&stattab=map
  • Last taxonomy: Kribbella
  • 16S sequence: JN038072
  • Sequence Identity:
  • Total samples: 1253
  • soil counts: 924
  • aquatic counts: 28
  • animal counts: 41
  • plant counts: 260

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
21432L1German classification
206231Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20623
  • description: Kribbella shirazensis strain UTMC 693 16S ribosomal RNA gene, partial sequence
  • accession: JN038072
  • length: 1424
  • database: ena
  • NCBI tax ID: 1105143

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kribbella shirazensis DSM 45490GCA_011761605contigncbi1105143
66792Kribbella shirazensis strain DSM 454901105143.3wgspatric1105143
66792Kribbella shirazensis DSM 454902827946139draftimg1105143

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.505yes
flagellatedno97.912yes
gram-positiveyes86.644no
anaerobicno99.216yes
aerobicyes89.454yes
halophileno96.488yes
spore-formingyes83.087yes
thermophileno98.177yes
glucose-utilyes88.113yes
glucose-fermentno86.071no

External links

@ref: 20623

culture collection no.: DSM 45490, CCUG 61792, UTMC 693

straininfo link

  • @ref: 88188
  • straininfo: 401183

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23524355Kribbella shirazensis sp. nov., isolated from Iranian soil.Mohammadipanah F, Hamedi J, Goker M, Fiebig A, Pukall R, Sproer C, Klenk HPInt J Syst Evol Microbiol10.1099/ijs.0.046847-02013Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Iran, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny28120200Kribbella soli sp. nov., isolated from soil.Ozdemir-Kocak F, Saygin H, Saricaoglu S, Cetin D, Guven K, Sproer C, Schumann P, Klenk HP, Sahin N, Isik KAntonie Van Leeuwenhoek10.1007/s10482-017-0830-x2017Actinobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Proteins/genetics, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, Essential, Multilocus Sequence Typing, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Vitamin K 2/analysisEnzymology

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20623Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45490Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45490)
21432Wink, J.Compendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweighttp://www.dsmz.de/microorganisms/wink_pdf/DSM45490.pdf
30886Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172721628776041
62710Curators of the CCUGhttps://www.ccug.se/strain?id=61792Culture Collection University of Gothenburg (CCUG) (CCUG 61792)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66793Mukherjee et al.GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life10.1038/nbt.388628604660 35: 676-683 2017
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88188Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID401183.1