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/bacdive12510.20250331.9.3

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

@refgram stainconfidence
125438negative97.728
125439negative97.2

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

@refgrowthtypetemperature
17342positivegrowth37
55031positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
17342anaerobe
55031anaerobe

spore formation

@refspore formationconfidence
125438no94.5
125439no99.3

metabolite utilization

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

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
6836735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
17342catalase-1.11.1.6
17342cytochrome-c oxidase-1.9.3.1
68380serine arylamidase-
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380glutamate decarboxylase-4.1.1.15
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
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 13863AB5476561451nuccore887901
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 sequenceGQ496515656nuccore887901
17342O.catoniae 16S rRNA geneX828231470nuccore887901
124043Porphyromonas catoniae ATCC 51270 gene for 16S rRNA, partial sequence.LC752304579nuccore887901
124043Porphyromonas catoniae JCM 13863 gene for 16S rRNA, partial sequence.LC752377579nuccore887901

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.728no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes65.741yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no86.899no
125438spore-formingspore-formingAbility to form endo- or exosporesno94.5no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.779yes
125438motile2+flagellatedAbility to perform flagellated movementno89.095no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.3
125439BacteriaNetmotilityAbility to perform movementyes55.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe78.2

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
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
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1