Strain identifier

BacDive ID: 11082

Type strain: Yes

Species: Kribbella sancticallisti

Strain history: DSM 19602 <-- C. Urzì BC633.

NCBI tax ID(s): 460087 (species)

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General

@ref: 8205

BacDive-ID: 11082

DSM-Number: 19602

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

description: Kribbella sancticallisti DSM 19602 is an aerobe, spore-forming, mesophilic bacterium that was isolated from tufacean surface, catacomb St. callistus.

NCBI tax id

  • NCBI tax id: 460087
  • Matching level: species

strain history

@refhistory
8205<- C. Urzi; BC633
67770DSM 19602 <-- C. Urzì BC633.

doi: 10.13145/bacdive11082.20230509.8.1

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 sancticallisti
  • full scientific name: Kribbella sancticallisti Urzì et al. 2008

@ref: 8205

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kribbellaceae

genus: Kribbella

species: Kribbella sancticallisti

full scientific name: Kribbella sancticallisti Urzì et al. 2008

type strain: yes

Morphology

cell morphology

  • @ref: 32517
  • gram stain: positive
  • cell width: 0.51 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18339Cream (9001)10-14 daysISP 2
18339Cream (9001)10-14 daysISP 3
18339Cream (9001)10-14 daysISP 4
18339Cream (9001)10-14 daysISP 5
18339Cream (9001)10-14 daysISP 6
18339Cream (9001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18339noISP 2
18339noISP 3
18339noISP 4
18339noISP 5
18339noISP 6
18339noISP 7

pigmentation

  • @ref: 32517
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8205R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
18339ISP 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
18339ISP 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:
18339ISP 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
18339ISP 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
18339ISP 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
18339ISP 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

culture temp

@refgrowthtypetemperaturerange
8205positivegrowth28mesophilic
18339positiveoptimum28mesophilic
32517positivegrowth10-37
32517positiveoptimum10-37
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32517positivegrowth05-10alkaliphile
32517positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32517
  • oxygen tolerance: aerobe

spore formation

  • @ref: 32517
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
32517NaClpositivegrowth0-5 %
32517NaClpositiveoptimum0-5 %

observation

@refobservation
32517aggregates in chains
67770quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3251722599arabinose+carbon source
3251728757fructose+carbon source
3251728260galactose+carbon source
3251724265gluconate+carbon source
3251717754glycerol+carbon source
3251717716lactose+carbon source
3251725115malate+carbon source
3251717306maltose+carbon source
3251729864mannitol+carbon source
3251737684mannose+carbon source
32517506227N-acetylglucosamine+carbon source
3251716634raffinose+carbon source
3251726546rhamnose+carbon source
3251717992sucrose+carbon source
3251718222xylose+carbon source
325174853esculin+hydrolysis
3251717632nitrate+reduction

enzymes

@refvalueactivityec
32517catalase+1.11.1.6
32517cytochrome oxidase+1.9.3.1
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 zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18339+++++----+-++-+++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8205tufacean surface, catacomb St. callistusRomeItalyITAEurope
67770Tufacean surfaces in the Roman catacombs of St CallistusRomeItalyITAEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Environmental#Terrestrial#Geologic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82051Risk group (German classification)
183391German classification

Sequence information

16S sequences

  • @ref: 8205
  • description: Kribbella sancallistae partial 16S rRNA gene, type strain BC633T
  • accession: AM778577
  • length: 1380
  • database: ena
  • NCBI tax ID: 460087

External links

@ref: 8205

culture collection no.: DSM 19602, JCM 14969, BC 633, NBRC 105865

straininfo link

  • @ref: 80331
  • straininfo: 402973

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18768610Kribbella catacumbae sp. nov. and Kribbella sancticallisti sp. nov., isolated from whitish-grey patinas in the catacombs of St Callistus in Rome, Italy.Urzi C, De Leo F, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.65613-02008Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/genetics, Diaminopimelic Acid/analysis, *Environmental Microbiology, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisGenetics
Phylogeny25842040Kribbella qitaiheensis sp. nov., a novel actinomycete isolated from soil.Guo L, Zhao J, Liu C, Han C, Bai L, Sun P, Li J, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-015-0446-y2015Actinobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Cell Wall/chemistry, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Geologic Sediments/microbiology, Glucose/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribose/analysis, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny30383522Kribbella monticola sp. nov., a novel actinomycete isolated from soil.Song W, Duan L, Zhao J, Jiang S, Guo X, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0030072018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8205Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19602)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19602
18339Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19602.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
32517Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2873728776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
80331Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402973.1StrainInfo: A central database for resolving microbial strain identifiers