Strain identifier

BacDive ID: 12510

Type strain: Yes

Species: Porphyromonas catoniae

Strain history: CCUG 41358 <-- NCTC 13056 <-- ATCC 51270 <-- L. V. Moore VPI N3B-3.

NCBI tax ID(s): 887901 (strain), 41976 (species)

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General

@ref: 17342

BacDive-ID: 12510

DSM-Number: 23684

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

description: Porphyromonas catoniae DSM 23684 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human oral cavity; gingival crevice of adult patient with periodontitis.

NCBI tax id

NCBI tax idMatching level
887901strain
41976species

strain history

@refhistory
17342<- JCM <- CCUG <- NCTC <- ATCC <- L. V. Moore, Virginia Polytechnical Institute and State University, Blacksburg, V., USA; VPI N3B-3
67770CCUG 41358 <-- NCTC 13056 <-- ATCC 51270 <-- L. V. Moore VPI N3B-3.

doi: 10.13145/bacdive12510.20230509.8.1

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 catoniae
  • full scientific name: Porphyromonas catoniae (Moore and Moore 1994) Willems and Collins 1995

  • synonyms

    • @ref: 20215
    • synonym: Oribaculum catoniae

@ref: 17342

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Porphyromonadaceae

genus: Porphyromonas

species: Porphyromonas catoniae

full scientific name: Porphyromonas catoniae (Moore and Moore 1994) Willems and Collins 1995 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.98

Culture and growth conditions

culture medium

  • @ref: 17342
  • name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/110
  • composition: Name: 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
17342positivegrowth37mesophilic
55031positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
17342anaerobe
55031anaerobe

spore formation

@refspore formationconfidence
69481no93
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose-builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
17342catalase-1.11.1.6
17342cytochrome-c oxidase-1.9.3.1
68380serine arylamidase-
68380glutamyl-glutamate 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
68380glutamate decarboxylase-4.1.1.15
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-
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
17342--------------+-----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
17342---+/--+---+/----+/---+--+----+----

Isolation, sampling and environmental information

isolation

@refsample type
17342human oral cavity; gingival crevice of adult patient with periodontitis
55031Human gingival crevice of adult patient
67770Human gingival crevice of adult patient

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Host#Human
#Host Body-Site#Oral cavity and airways#Gingiva

taxonmaps

  • @ref: 69479
  • File name: preview.99_1126.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_156;96_658;97_761;98_880;99_1126&stattab=map
  • Last taxonomy: Porphyromonas catoniae subclade
  • 16S sequence: AB547656
  • Sequence Identity:
  • Total samples: 19171
  • soil counts: 334
  • aquatic counts: 354
  • animal counts: 18353
  • plant counts: 130

Safety information

risk assessment

  • @ref: 17342
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Porphyromonas catoniae gene for 16S ribosomal RNA, partial sequence, strain: JCM 13863AB5476561451ena887901
20218Porphyromonas catoniae strain CCUG 41358 clone 1 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGQ496515656ena887901
17342O.catoniae 16S rRNA geneX828231470ena887901

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Porphyromonas catoniae ATCC 51270887901.3wgspatric887901
66792Porphyromonas catoniae ATCC 512702558860281draftimg887901
67770Porphyromonas catoniae ATCC 51270GCA_000565015contigncbi887901

GC content

@refGC-contentmethod
1734249
1734251.0sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
motileno91.085no
flagellatedno97.01no
gram-positiveno97.163no
anaerobicyes96.514yes
halophileno75.305no
spore-formingno98.081no
thermophileno99.18yes
glucose-utilyes80.363no
aerobicno98.693yes
glucose-fermentyes59.76no

External links

@ref: 17342

culture collection no.: DSM 23684, ATCC 51270, CCUG 41358, JCM 13863, NCTC 13056, VPI N3B-3

straininfo link

  • @ref: 81729
  • straininfo: 42889

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8186083Oribaculum catoniae gen. nov., sp. nov.; Catonella morbi gen. nov., sp. nov.; Hallella seregens gen. nov., sp. nov.; Johnsonella ignava gen. nov., sp. nov.; and Dialister pneumosintes gen. nov., comb. nov., nom. rev., Anaerobic gram-negative bacilli from the human gingival crevice.Moore LV, Moore WEInt J Syst Bacteriol10.1099/00207713-44-2-1871994Bacterial Typing Techniques, Fatty Acids/analysis, Gingival Pocket/*microbiology, Gingivitis/*microbiology, Gram-Negative Anaerobic Bacteria/*classification/isolation & purification, Gram-Negative Bacterial Infections/*microbiology, Humans, Periodontitis/*microbiologyPathogenicity
Phylogeny25933621Porphyromonas pasteri sp. nov., isolated from human saliva.Sakamoto M, Li D, Shibata Y, Takeshita T, Yamashita Y, Ohkuma MInt J Syst Evol Microbiol10.1099/ijs.0.0002942015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Humans, Molecular Sequence Data, *Phylogeny, Porphyromonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Saliva/*microbiology, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17342Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23684)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23684
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
55031Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 41358)https://www.ccug.se/strain?id=41358
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
81729Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42889.1StrainInfo: A central database for resolving microbial strain identifiers