Strain identifier

BacDive ID: 132059

Type strain: Yes

Species: Porphyromonas circumdentaria

Strain history: CCUG 41934 <-- NCTC 12469 <-- D. N. Love VPB 3329.

NCBI tax ID(s): 29524 (species)

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General

@ref: 23850

BacDive-ID: 132059

DSM-Number: 103022

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

description: Porphyromonas circumdentaria DSM 103022 is an anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from cat, subcutaneous abscess.

NCBI tax id

  • NCBI tax id: 29524
  • Matching level: species

strain history

@refhistory
23850<- NCTC <- D. N. Love, University of Sydney; VPB 3329
67770CCUG 41934 <-- NCTC 12469 <-- D. N. Love VPB 3329.

doi: 10.13145/bacdive132059.20230509.8.1

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 circumdentaria
  • full scientific name: Porphyromonas circumdentaria Love et al. 1992

@ref: 23850

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Porphyromonadaceae

genus: Porphyromonas

species: Porphyromonas circumdentaria

full scientific name: Porphyromonas circumdentaria Love et al. 1992

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.898

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
23850COLUMBIA 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
23850CHOPPED 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
23850positivegrowth37mesophilic
55269positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
55269anaerobe
69480anaerobe99.225

spore formation

@refspore formationconfidence
69481no100
69480no100

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-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
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
23850---------------++--+----+--+/--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
23850cat, subcutaneous abscessAustraliaAUSAustralia and Oceania
55269Cat abscess,subcutaneous1978
67770Subcutaneous abscess of a cat

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Felidae (Cat)
#Host Body-Site#Other#Abscess

taxonmaps

  • @ref: 69479
  • File name: preview.99_4948.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16039;96_634;97_737;98_856;99_4948&stattab=map
  • Last taxonomy: Porphyromonas circumdentaria
  • 16S sequence: AB547657
  • Sequence Identity:
  • Total samples: 3485
  • soil counts: 73
  • aquatic counts: 40
  • animal counts: 3347
  • plant counts: 25

Safety information

risk assessment

  • @ref: 23850
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
23850Porphyromonas circumdentaria strain NCTC 12469 16S ribosomal RNA gene, partial sequenceL261021470ena29524
67770Porphyromonas circumdentaria gene for 16S ribosomal RNA, partial sequence, strain: JCM 13864AB5476571476ena29524

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Porphyromonas circumdentaria ATCC 51356GCA_900167105scaffoldncbi29524
66792Porphyromonas circumdentaria DSM 103022GCA_014206885contigncbi29524
66792Porphyromonas circumdentaria strain ATCC 5135629524.4wgspatric29524
66792Porphyromonas circumdentaria strain DSM 10302229524.6wgspatric29524
66792Porphyromonas circumdentaria ATCC 513562582581320draftimg29524
66792Porphyromonas circumdentaria DSM 1030222828459078draftimg29524

GC content

  • @ref: 67770
  • GC-content: 40-42
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.863no
flagellatedno96.637no
gram-positiveno95.912no
anaerobicyes98.532yes
aerobicno98.842yes
halophileno77.153no
spore-formingno97.11no
thermophileno97.869yes
glucose-utilyes84.885no
glucose-fermentno52.514no

External links

@ref: 23850

culture collection no.: DSM 103022, ATCC 51356, CCUG 41934, JCM 13864, NCTC 12469, VPB 3329

straininfo link

  • @ref: 90417
  • straininfo: 42946

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1503973Description of Porphyromonas circumdentaria sp. nov. and reassignment of Bacteroides salivosus (Love, Johnson, Jones, and Calverley 1987) as Porphyromonas (Shah and Collins 1988) salivosa comb. nov.Love DN, Bailey GD, Collings S, Briscoe DAInt J Syst Bacteriol10.1099/00207713-42-3-4341992Animals, Bacteroides/*classification/physiology/ultrastructure, Bacteroides Infections/microbiology/veterinary, Cat Diseases/microbiology, Cats, DNA, Bacterial/chemistry, Enzymes/metabolism, Fatty Acids/biosynthesis, Gingiva/microbiology, Microscopy, Electron, Nucleic Acid HybridizationEnzymology
Phylogeny7981094Porphyromonas gingivicanis sp. nov. and Porphyromonas crevioricanis sp. nov., isolated from beagles.Hirasawa M, Takada KInt J Syst Bacteriol10.1099/00207713-44-4-6371994Animals, DNA, Bacterial/analysis, Dogs/*microbiology, Gingiva/microbiology, Porphyromonas/genetics/*isolation & purification/metabolismEnzymology
Phylogeny8186085Porphyromonas canoris sp. nov., an asaccharolytic, black-pigmented species from the gingival sulcus of dogs.Love DN, Karjalainen J, Kanervo A, Forsblom B, Sarkiala E, Bailey GD, Wigney DI, Jousimies-Somer HInt J Syst Bacteriol10.1099/00207713-44-2-2041994Animals, Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial, Dental Plaque/*microbiology, Dogs, Fatty Acids/analysis, Gingiva/*microbiology, Gingival Diseases/microbiology/*veterinary, Nucleic Acid Hybridization, Pigments, Biological, Porphyromonas/*classification/isolation & purificationMetabolism
Pathogenicity11386420Structural characterization of the O-antigenic polysaccharide chain of Porphyromonas circumdentaria NCTC 12469.Matsuo K, Isogai E, Araki YMicrobiol Immunol10.1111/j.1348-0421.2001.tb02622.x2001Animals, Carbohydrate Sequence, Humans, Hydrolysis, Magnetic Resonance Spectroscopy, Molecular Sequence Data, O Antigens/*chemistry, Porphyromonas/*chemistry/*immunology/pathogenicityGenetics

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
23850Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103022Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103022)
55269Curators of the CCUGhttps://www.ccug.se/strain?id=41934Culture Collection University of Gothenburg (CCUG) (CCUG 41934)
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
90417Reimer, 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-ID42946.1