Strain identifier

BacDive ID: 132848

Type strain: Yes

Species: Porphyromonas cangingivalis

Strain history: STAFF <-- ATCC 700135 <-- NCTC 12856 <-- AHN 4309.

NCBI tax ID(s): 1236520 (strain), 36874 (species)

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General

@ref: 24636

BacDive-ID: 132848

DSM-Number: 104739

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, animal pathogen

description: Porphyromonas cangingivalis DSM 104739 is an anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from periodontal pocket; dog.

NCBI tax id

NCBI tax idMatching level
1236520strain
36874species

strain history

@refhistory
24636<- NCTC; NCTC 12856
67770STAFF <-- ATCC 700135 <-- NCTC 12856 <-- AHN 4309.

doi: 10.13145/bacdive132848.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Porphyromonadaceae
  • genus: Porphyromonas
  • species: Porphyromonas cangingivalis
  • full scientific name: Porphyromonas cangingivalis Collins et al. 1994

@ref: 24636

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Porphyromonadaceae

genus: Porphyromonas

species: Porphyromonas cangingivalis

full scientific name: Porphyromonas cangingivalis Collins et al. 1994

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.95

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24636COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
24636CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
24636positivegrowth37mesophilic
57824positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
57824anaerobe
69480anaerobe98.806

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan+energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase+4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
24636---------------++--+--+/--+--+-
24636---------------++--+--+/--+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24636periodontal pocket; dog
57824Dog periodontal pocketHelsinki ?FinlandFINEurope
67770Periodontal pocket

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Canidae (Dog)
#Host Body-Site#Oral cavity and airways#Periodontal pocket

taxonmaps

  • @ref: 69479
  • File name: preview.99_283.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15883;96_197;97_214;98_239;99_283&stattab=map
  • Last taxonomy: Porphyromonas cangingivalis subclade
  • 16S sequence: X76259
  • Sequence Identity:
  • Total samples: 15871
  • soil counts: 347
  • aquatic counts: 354
  • animal counts: 15011
  • plant counts: 159

Safety information

risk assessment

  • @ref: 24636
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
24636Porphyromonas cangingivalis gene for 16S ribosomal RNA, partial sequence, strain: JCM 15983AB5476541493ena36874
24636P.cangingivalis (VPB 4874) 16S rRNA geneX762591484ena36874

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Porphyromonas cangingivalis NCTC12856GCA_900638305completencbi36874
66792Porphyromonas cangingivalis JCM 159831236520.3wgspatric1236520
66792Porphyromonas cangingivalis strain ATCC 70013536874.13wgspatric36874
66792Porphyromonas cangingivalis strain NCTC1285636874.15completepatric36874
66792Porphyromonas cangingivalis JCM 159832585427887draftimg1236520
66792Porphyromonas cangingivalis ATCC 7001352585428082draftimg36874
67770Porphyromonas cangingivalis JCM 15983GCA_000614355contigncbi1236520
67770Porphyromonas cangingivalis ATCC 700135GCA_900167355scaffoldncbi36874

GC content

@refGC-contentmethod
2463655
6777055thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.569no
gram-positiveno96.401no
anaerobicyes97.78no
aerobicno96.808yes
halophileno78.596no
spore-formingno96.058no
thermophileno98.647yes
glucose-utilyes81.567no
motileno89.283no
glucose-fermentno58.911no

External links

@ref: 24636

culture collection no.: DSM 104739, AHN 4309, ATCC 700135, JCM 15983, NCTC 12856, CCUG 47700, JCM 13862, VPB 4874

straininfo link

  • @ref: 91136
  • straininfo: 45403

literature

  • topic: Pathogenicity
  • Pubmed-ID: 33267882
  • title: A polymicrobial biofilm model for testing the antimicrobial potential of a nisin-biogel for canine periodontal disease control.
  • authors: Cunha E, Rebelo S, Carneiro C, Tavares L, Carreira LM, Oliveira M
  • journal: BMC Vet Res
  • DOI: 10.1186/s12917-020-02646-3
  • year: 2020
  • mesh: Animals, Anti-Bacterial Agents/administration & dosage, Biofilms/*drug effects, Dog Diseases/*drug therapy, Dogs, Gram-Negative Bacteria/drug effects, Gram-Positive Bacteria/drug effects, Nisin/*pharmacology, Periodontal Diseases/drug therapy/microbiology/*veterinary

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24636Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104739Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104739)
57824Curators of the CCUGhttps://www.ccug.se/strain?id=47700Culture Collection University of Gothenburg (CCUG) (CCUG 47700)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
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
91136Reimer, 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-ID45403.1