Strain identifier

BacDive ID: 4259

Type strain: Yes

Species: Dietzia papillomatosis

Strain Designation: N 1280

Strain history: IFM 10921 <-- DSM 44961 <-- A. L. Jones <-- R. J. Koerner N 1280.

NCBI tax ID(s): 1349764 (strain), 282305 (species)

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General

@ref: 12214

BacDive-ID: 4259

DSM-Number: 44961

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, human pathogen

description: Dietzia papillomatosis N 1280 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from skin scrapings of a 17-year-old boy with CRP.

NCBI tax id

NCBI tax idMatching level
282305species
1349764strain

strain history

@refhistory
12214<- A. L. Jones <- R. Koerner; N 1280
67770IFM 10921 <-- DSM 44961 <-- A. L. Jones <-- R. J. Koerner N 1280.

doi: 10.13145/bacdive4259.20230509.8.1

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 papillomatosis
  • full scientific name: Dietzia papillomatosis Jones et al. 2008

@ref: 12214

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dietziaceae

genus: Dietzia

species: Dietzia papillomatosis

full scientific name: Dietzia papillomatosis Jones et al. 2008

strain designation: N 1280

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
32240positiveno
69480no94.381
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19895Bright red orange10-14 daysISP 2
1989510-14 daysISP 3
1989510-14 daysISP 4
1989510-14 daysISP 5
19895Pastel orange10-14 daysISP 6
19895Pastel orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19895noISP 2
19895noISP 3
19895noISP 4
19895noISP 5
19895noISP 6
19895noISP 7

pigmentation

  • @ref: 32240
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12214GYM 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
12214TRYPTICASE 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
19895ISP 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
19895ISP 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:
19895ISP 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
19895ISP 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
19895ISP 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
19895ISP 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
19895positiveoptimum28mesophilic
12214positivegrowth28mesophilic
32240positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
12214aerobe
32240aerobe

spore formation

@refspore formationconfidence
32240no
69481yes90
69480no99.971

halophily

  • @ref: 32240
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 07-08 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1989517234glucose-
1989522599arabinose-
1989517992sucrose-
1989518222xylose-
1989517268myo-inositol-
1989529864mannitol-
1989528757fructose+
1989526546rhamnose-
1989516634raffinose-
1989562968cellulose-
6836925115malate-assimilation
6836927689decanoate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

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
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
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19895+-+-+-+--+----+----
12214++++/-+----++/----+/------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
12214+---+---------+/--+/----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12214skin scrapings of a 17-year-old boy with CRPUnited KingdomGBREurope
67770Skin of an immunocompetent patient with confluent and reticulated papillomatosis

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Infection#Patient
#Host Body-Site#Organ#Skin, Nail, Hair
#Host#Human#Male

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12214yes, in single cases1Risk group (German classification)
198951Risk group (german classification)

Sequence information

16S sequences

  • @ref: 12214
  • description: Dietzia papillomatosis strain N 1280 16S ribosomal RNA gene, partial sequence
  • accession: AY643401
  • length: 1438
  • database: ena
  • NCBI tax ID: 282305

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dietzia papillomatosis NBRC 1050451349764.3wgspatric1349764
66792Dietzia papillomatosis NBRC 1050452731957607draftimg1349764
67770Dietzia papillomatosis NBRC 105045GCA_001570845contigncbi1349764

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes90no
motileno95.777yes
gram-positiveyes89.783yes
anaerobicno99.177no
halophileyes59.725yes
spore-formingno88.8yes
glucose-utilyes85.451yes
aerobicyes91.59yes
flagellatedno98.38yes
thermophileno98.851yes
glucose-fermentno86.522yes

External links

@ref: 12214

culture collection no.: DSM 44961, NCIMB 14145, JCM 15317, IFM 10921, NBRC 105045

straininfo link

  • @ref: 73754
  • straininfo: 297461

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175685Dietzia papillomatosis sp. nov., a novel actinomycete isolated from the skin of an immunocompetent patient with confluent and reticulated papillomatosis.Jones AL, Koerner RJ, Natarajan S, Perry JD, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.65178-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Actinomycetales Infections/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, Genes, rRNA, Genotype, Humans, Immunocompetence, Molecular Sequence Data, Papilloma/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Skin/*microbiology, Species SpecificityGenetics
27601929Confluent and reticulated papillomatosis: diagnostic and treatment challenges.Lim JH, Tey HL, Chong WSClin Cosmet Investig Dermatol10.2147/CCID.S920512016

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12214Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44961)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44961
19895Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44961.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
32240Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2848128776041
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/
68369Automatically annotated from API 20NE
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
73754Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297461.1StrainInfo: A central database for resolving microbial strain identifiers