Strain identifier

BacDive ID: 11081

Type strain: Yes

Species: Kribbella catacumbae

Strain history: DSM 19601 <-- C. Urzì BC631.

NCBI tax ID(s): 1122138 (strain), 460086 (species)

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General

@ref: 8204

BacDive-ID: 11081

DSM-Number: 19601

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

description: Kribbella catacumbae DSM 19601 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from catacomb of St. Callistus.

NCBI tax id

NCBI tax idMatching level
1122138strain
460086species

strain history

@refhistory
8204<- C. Urzi; BC631
67770DSM 19601 <-- C. Urzì BC631.

doi: 10.13145/bacdive11081.20230509.8.1

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

@ref: 8204

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kribbellaceae

genus: Kribbella

species: Kribbella catacumbae

full scientific name: Kribbella catacumbae Urzì et al. 2008 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
32517positive0.36 µmrod-shapedno
69480no92.119
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
18338Pastel yellow (1034)10-14 daysISP 2
18338Beige (1001)10-14 daysISP 3
18338Beige (1001)10-14 daysISP 4
18338Beige (1001)10-14 daysISP 5
18338Beige (1001)10-14 daysISP 6
18338Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
18338noISP 2
18338yesISP 3Aerial MyceliumCream
18338yesISP 4Aerial MyceliumCream
18338noISP 5
18338noISP 6
18338noISP 7

pigmentation

  • @ref: 32517
  • production: no

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_19601_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19601_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19601_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19601_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19601_5.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19601_6.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8204R2A 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
18338ISP 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
18338ISP 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:
18338ISP 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
18338ISP 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
18338ISP 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
18338ISP 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
8204positivegrowth28mesophilic
18338positiveoptimum28mesophilic
32517positivegrowth10-30
32517positiveoptimum10-30
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32517positivegrowth05-10alkaliphile
32517positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32517
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32517yes
69481yes100
69480yes92.928

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
3251717234glucose+carbon source
3251717754glycerol+carbon source
3251717716lactose+carbon source
3251717306maltose+carbon source
3251729864mannitol+carbon source
3251737684mannose+carbon source
3251726546rhamnose+carbon source
3251717992sucrose+carbon source
3251718222xylose+carbon source

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
18338++++++-++++++-+++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8204catacomb of St. CallistusRomeItalyITAEurope
67770Roman catacombs of St CallistusRomeItalyITAEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Built environment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82041Risk group (German classification)
183381German classification

Sequence information

16S sequences

  • @ref: 8204
  • description: Kribbella catacumbae partial 16S rRNA gene, type strain BC631T
  • accession: AM778575
  • length: 1442
  • database: ena
  • NCBI tax ID: 460086

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kribbella catacumbae DSM 196011122138.3wgspatric1122138
66792Kribbella catacumbae DSM 196012515154140draftimg1122138
67770Kribbella catacumbae DSM 19601GCA_000372465contigncbi1122138

GC content

  • @ref: 67770
  • GC-content: 67.5
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.714yes
flagellatedno97.895yes
gram-positiveyes87.516yes
anaerobicno99.353yes
halophileno96.204no
spore-formingyes88.237no
thermophileno99.093yes
glucose-utilyes86.122yes
aerobicyes93.503no
glucose-fermentno89.125no

External links

@ref: 8204

culture collection no.: DSM 19601, JCM 14968, BC 631, NBRC 105864

straininfo link

  • @ref: 80330
  • straininfo: 400191

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_referencepubmedjournal
8204Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19601)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19601
18338Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19601.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
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
80330Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400191.1StrainInfo: A central database for resolving microbial strain identifiers