Strain identifier

BacDive ID: 24337

Type strain: No

Species: Porphyromonas gingivalis

Strain Designation: HG66

Strain history: <- J. Potempa <- R. Arnold, Emory University; HG66

NCBI tax ID(s): 837 (species)

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General

@ref: 20739

BacDive-ID: 24337

DSM-Number: 28984

keywords: genome sequence, Bacteria, anaerobe, mesophilic, Gram-negative, human pathogen

description: Porphyromonas gingivalis HG66 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human oral cavity.

NCBI tax id

  • NCBI tax id: 837
  • Matching level: species

strain history

  • @ref: 20739
  • history: <- J. Potempa <- R. Arnold, Emory University; HG66

doi: 10.13145/bacdive24337.20250331.9.3

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 gingivalis
  • full scientific name: Porphyromonas gingivalis (Coykendall et al. 1980) Shah and Collins 1988

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides gingivalis

@ref: 20739

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Porphyromonadaceae

genus: Porphyromonas

species: Porphyromonas gingivalis

full scientific name: Porphyromonas gingivalis (Coykendall et al. 1980) Shah and Collins 1988 emend. Hahnke et al. 2016

strain designation: HG66

type strain: no

Morphology

cell morphology

@refgram stainconfidence
125438negative95.437
125439negative98.4

colony morphology

  • @ref: 20739
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20739COLUMBIA 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
20739CHOPPED 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

  • @ref: 20739
  • growth: positive
  • type: growth
  • temperature: 37

Physiology and metabolism

oxygen tolerance

  • @ref: 20739
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
125438no93.996
125439no98.5

metabolite utilization

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

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380serine arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine 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
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380alpha-galactosidase-3.2.1.22
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
20739---+/------+-----++--+----+--+-
20739---++/-----+-----++--+--+/--+--+/--
20739-+-++/-----+-----++--+--+/--+--+-

Isolation, sampling and environmental information

isolation

  • @ref: 20739
  • sample type: human oral cavity
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways
#Host Body-Site#Oral cavity and airways#Mouth

Safety information

risk assessment

  • @ref: 20739
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Porphyromonas gingivalis HG66GCA_000739415chromosomencbi837
66792Porphyromonas gingivalis HG662597490155draftimg837

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno95.437no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes85.233no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no91.435yes
125438spore-formingspore-formingAbility to form endo- or exosporesno93.996no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.741yes
125438motile2+flagellatedAbility to perform flagellated movementno87.074no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.5
125439BacteriaNetmotilityAbility to perform movementno61.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative aerobe65.5

External links

@ref: 20739

culture collection no.: DSM 28984

straininfo link

  • @ref: 88263
  • straininfo: 407947

literature

  • topic: Genetics
  • Pubmed-ID: 25291768
  • title: Genome Sequence of Porphyromonas gingivalis Strain HG66 (DSM 28984).
  • authors: Siddiqui H, Yoder-Himes DR, Mizgalska D, Nguyen KA, Potempa J, Olsen I
  • journal: Genome Announc
  • DOI: 10.1128/genomeA.00947-14
  • year: 2014

Reference

@idauthorstitledoi/urlcatalogue
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
20739Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28984Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28984)
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
68380Automatically annotated from API rID32A
88263Reimer, 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-ID407947.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG