Strain identifier

BacDive ID: 12509

Type strain: Yes

Species: Porphyromonas endodontalis

Strain Designation: HG370

Strain history: Tokyo Med. Dent. Univ. <-- ATCC 35406 <-- T. J. M. van Steenbergen HG 370.

NCBI tax ID(s): 553175 (strain), 28124 (species)

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General

@ref: 17688

BacDive-ID: 12509

DSM-Number: 24491

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Porphyromonas endodontalis HG370 is an anaerobe, mesophilic bacterium that was isolated from infected dental root canal.

NCBI tax id

NCBI tax idMatching level
28124species
553175strain

strain history

@refhistory
17688<- NCTC <- T. J. M. van Steenbergen; HG370
67770Tokyo Med. Dent. Univ. <-- ATCC 35406 <-- T. J. M. van Steenbergen HG 370.

doi: 10.13145/bacdive12509.20230509.8.1

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 endodontalis
  • full scientific name: Porphyromonas endodontalis (van Steenbergen et al. 1984) Shah and Collins 1988

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides endodontalis

@ref: 17688

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Porphyromonadaceae

genus: Porphyromonas

species: Porphyromonas endodontalis

full scientific name: Porphyromonas endodontalis (van Steenbergen et al. 1984) Shah and Collins 1988 emend. Hahnke et al. 2016

strain designation: HG370

type strain: yes

Morphology

colony morphology

@refincubation period
176881-2 days
464856-8 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17688COLUMBIA 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
17688CHOPPED 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
17688positivegrowth37mesophilic
46485positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
17688anaerobe
46485anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836717057cellobiose-builds acid from
683675291gelatin+hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836716199urea-hydrolysis
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
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
68367gelatinase+
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
17688+---------+---------
17688--+++++---++/-+-+----+

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
17688---------------++--+----+----
17688---------+/------++--+----+--+/--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17688infected dental root canalAmsterdamNetherlandsNLDEurope
46485Infected root canal
67770Infected root canal

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host Body-Site#Oral cavity and airways#Tooth

Safety information

risk assessment

  • @ref: 17688
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Porphyromonas endodontalis gene for 16S ribosomal RNA, partial sequence, strain: JCM 8526AB5476591435ena28124
20218Porphyromonas endodontalis strain ATCC 35406 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY546477735ena28124
20218Porphyromonas endodontalis ATCC 35406 16S ribosomal RNA gene, complete sequenceL164911475ena28124
17688Porphyromonas endodontalis ATCC 35406 16S ribosomal RNA gene, partial sequenceAY2537281441ena28124

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Porphyromonas endodontalis ATCC 35406553175.3wgspatric553175
66792Porphyromonas endodontalis strain FDAARGOS_150628124.79completepatric28124
66792Porphyromonas endodontalis strain NCTC1305828124.3wgspatric28124
66792Porphyromonas endodontalis ATCC 35406643886148draftimg553175
66792Porphyromonas endodontalis NCTC 130582858648101draftimg28124
67770Porphyromonas endodontalis ATCC 35406GCA_000174815contigncbi553175
67770Porphyromonas endodontalis NCTC13058GCA_900454815contigncbi28124
66792Porphyromonas endodontalis strain FDAARGOS_150628124.82completepatric28124
66792Porphyromonas endodontalis strain FDAARGOS_150628124.80completepatric28124
66792Porphyromonas endodontalis strain FDAARGOS_150628124.81completepatric28124

GC content

@refGC-contentmethod
1768847.5sequence analysis
6777049.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.041no
gram-positiveno96.578no
anaerobicyes99.437no
halophileno85.819no
spore-formingno95.122no
glucose-utilyes78.088no
flagellatedno96.382no
aerobicno98.597no
thermophileno99.146no
glucose-fermentno50.78no

External links

@ref: 17688

culture collection no.: DSM 24491, ATCC 35406, JCM 8526, NCTC 13058, CCUG 16442, BCRC 14492

straininfo link

  • @ref: 81728
  • straininfo: 45021

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology1298803Characterization of total membrane protein of Porphyromonas endodontalis.Herweijer JA, Loos BG, Neiders MEJ Endod10.1016/s0099-2399(06)81334-81992Bacterial Proteins/analysis/*chemistry, Bacteroides/*chemistry/growth & development, Electrophoresis, Polyacrylamide Gel, Membrane Proteins/analysis/*chemistry
Pathogenicity1328059Immunochemical and biological characterization of outer membrane proteins of Porphyromonas endodontalis.Ogawa T, Kuribayashi S, Shimauchi H, Toda T, Hamada SInfect Immun10.1128/iai.60.11.4528-4533.19921992Antibodies, Bacterial/*immunology, Bacterial Outer Membrane Proteins/*immunology/isolation & purification, Gram-Negative Bacteria/chemistry/*immunology, Humans, Leukocytes, Mononuclear/immunology, Lipopolysaccharides/chemistry/immunology, Periapical Abscess/*microbiology, Periapical Granuloma/immunology, Porins, Radicular Cyst/immunologyEnzymology
Pathogenicity1855992Humoral immune response to an antigen from Porphyromonas gingivalis 381 in periodontal disease.Kurihara H, Nishimura F, Nakamura T, Nakagawa M, Tanimoto I, Nomura Y, Kokeguchi S, Kato K, Murayama YInfect Immun10.1128/iai.59.8.2758-2762.19911991Antibodies, Bacterial/*immunology, Antibodies, Monoclonal/immunology, Antigens, Bacterial/blood/*immunology, Bacteroides/*immunology, Bacteroides Infections/*immunology/microbiology, Blotting, Western, Humans, Immunohistochemistry, Periodontitis/*microbiology
Enzymology2370106Monoclonal antibody against a serotype antigen of Porphyromonas (Bacteroides) endodontalis and characteristics of the antigen.Hanazawa S, Sagiya T, Amano S, Nishikawa H, Kitano SInfect Immun10.1128/iai.58.8.2542-2546.19901990Animals, Antibodies, Bacterial/*biosynthesis/immunology, Antibodies, Monoclonal/*biosynthesis/immunology, Antibody Specificity, Antigens, Bacterial/*immunology/isolation & purification, Bacteroides/classification/*immunology, Chromatography, Gel, Chromatography, High Pressure Liquid, Electrophoresis, Polyacrylamide Gel, Immunoblotting, Mice, Mice, Inbred BALB C, Polysaccharides, Bacterial/immunology, SerotypingPhylogeny
Pathogenicity2762019The effect of subminimal inhibitory concentrations of antimicrobial agents on three bacterial mixtures.Lacroix JM, Mayrand DOral Microbiol Immunol10.1111/j.1399-302x.1989.tb00104.x1989Bacteria/drug effects/*metabolism, Bacteroides/drug effects, Capnocytophaga/drug effects, Eubacterium/drug effects, Fusobacterium/drug effects, Metronidazole/*pharmacology, Microbial Sensitivity Tests, Tetracycline/*pharmacologyMetabolism
Enzymology7894713Congo red binding by Porphyromonas gingivalis is mediated by a 66 kDa outer-membrane protein.Smalley JW, Birss AJ, McKee AS, Marsh PDMicrobiology (Reading)10.1099/00221287-141-1-2051995Bacterial Outer Membrane Proteins/isolation & purification/*metabolism, Congo Red/*metabolism, Electrophoresis, Polyacrylamide Gel, Endopeptidases/pharmacology, Genetic Variation, Kinetics, Molecular Weight, Polymyxin B/pharmacology, Porphyromonas/metabolism, Porphyromonas gingivalis/genetics/*metabolism/pathogenicity, Protein Binding, Species SpecificityMetabolism
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
Biotechnology8762538[Production and characterization of specific monoclonal antibody against Porphyromonas endodontalis].Xue Y, Sun C, Tan JZhonghua Kou Qiang Yi Xue Za Zhi1995Animals, Antibodies, Monoclonal/*biosynthesis, Antigens, Bacterial/immunology, Bacteroidaceae Infections/*microbiology, Dental Pulp/*microbiology, Female, Hybridomas/metabolism, Mice, Mice, Inbred BALB C, Periapical Abscess/*microbiology, Porphyromonas/*immunology/isolation & purification, Sensitivity and SpecificityMetabolism
Phylogeny9467401Isolation and characterization of a nonpigmented variant of Porphyromonas endodontalis.Suzuki K, Ikeda T, Nakamura H, Yoshimura FOral Microbiol Immunol10.1111/j.1399-302x.1997.tb00372.x1997Anti-Bacterial Agents/pharmacology, Bacterial Proteins/analysis, DNA, Bacterial/chemistry, Drug Resistance, Microbial, Escherichia coli/genetics, Microbial Sensitivity Tests, Pigmentation, Porphyromonas/classification/drug effects/*isolation & purification/physiology, Sequence Homology, Nucleic Acid, Vancomycin/pharmacologyEnzymology
Metabolism9693583Experimental root canal infections in conventional and germ-free mice.Sobrinho AP, Barros MH, Nicoli JR, Carvalho MA, Farias LM, Bambirra EA, Bahia MG, Vieira ECJ Endod10.1016/S0099-2399(98)80021-61998Animals, Antibiosis, Bacteria, Anaerobic/*growth & development/metabolism, Bacteriocins/metabolism, Dental Pulp Cavity/*microbiology, *Disease Models, Animal, Ecosystem, Enterococcus faecalis/growth & development/metabolism, Escherichia coli/growth & development/metabolism, Eubacterium/growth & development/metabolism, Fusobacterium nucleatum/growth & development/metabolism, Germ-Free Life, Mice, Peptostreptococcus/growth & development/metabolism, Porphyromonas/growth & development/metabolism
Phylogeny10635221Survey for collagenase gene prtC in Porphyromonas gingivalis and Porphyromonas endodontalis isolated from endodontic infections.Odell LJ, Baumgartner JC, Xia T, David LLJ Endod10.1016/S0099-2399(99)80379-31999*Bacterial Proteins, Bacterial Typing Techniques, Bacteroidaceae Infections/microbiology, Collagenases/*genetics, DNA, Bacterial/genetics, Dental Pulp Cavity/microbiology, Dental Pulp Diseases/*microbiology, *Genes, Bacterial, Humans, Microbial Collagenase/*genetics, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, Porphyromonas/classification/*enzymology/*genetics, Porphyromonas gingivalis/classification/enzymology/genetics, RNA, Ribosomal, 16S/geneticsPathogenicity
Enzymology11737654The purification and characterization of an 88-kDa Porphyromonas endodontalis 35406 protease.Rosen G, Shoshani M, Naor R, Sela MNOral Microbiol Immunol10.1034/j.1399-302x.2001.160602.x2001Aminopeptidases/isolation & purification, Angiotensins/chemistry, Bradykinin/chemistry, Chromogenic Compounds/chemistry, Collagen Type IV/chemistry, Cystinyl Aminopeptidase/isolation & purification, Electrophoresis, Polyacrylamide Gel, Endopeptidases/chemistry/*isolation & purification, Fibrinogen/chemistry, Fibronectins/chemistry, Hot Temperature, Humans, Hydrogen-Ion Concentration, Isoelectric Focusing, Lysine Carboxypeptidase/isolation & purification, Molecular Weight, Oxidants/chemistry, Oxidation-Reduction, Phenylalanine/chemistry, Porphyromonas/classification/*enzymology, Sodium Dodecyl Sulfate/chemistry, Surface-Active Agents/chemistry, Temperature, Tyrosine/chemistry, Vasopressins/chemistryPhylogeny
Cultivation12059938Invasion of vascular cells in vitro by Porphyromonas endodontalis.Dorn BR, Harris LJ, Wujick CT, Vertucci FJ, Progulske-Fox AInt Endod J10.1046/j.0143-2885.2001.00489.x2002Bacteroidaceae Infections/microbiology, Cell Culture Techniques, Coronary Vessels/cytology/microbiology, Culture Media, Dental Pulp Diseases/microbiology, Endothelium, Vascular/cytology/*microbiology, Escherichia coli/pathogenicity/physiology, Humans, Microscopy, Electron, Muscle, Smooth, Vascular/cytology/microbiology, Porphyromonas/classification/pathogenicity/*physiology, Porphyromonas gingivalis/pathogenicity/physiology, Prevotella/classification/pathogenicity/physiology, Prevotella intermedia/pathogenicity/physiologyPathogenicity
Pathogenicity18814211Antibacterial activity of [10]-gingerol and [12]-gingerol isolated from ginger rhizome against periodontal bacteria.Park M, Bae J, Lee DSPhytother Res10.1002/ptr.24732008Anti-Bacterial Agents/*pharmacology, Catechols/chemistry/*pharmacology, Chromatography, High Pressure Liquid, Fatty Alcohols/chemistry/*pharmacology, Ginger/chemistry, Humans, Microbial Sensitivity Tests, Periodontitis/microbiology, Plant Extracts/pharmacology, Porphyromonas endodontalis/*drug effects, Porphyromonas gingivalis/*drug effects, Prevotella intermedia/*drug effects, Spectrometry, Mass, Electrospray Ionization
Enzymology21896480Asp- and Glu-specific novel dipeptidyl peptidase 11 of Porphyromonas gingivalis ensures utilization of proteinaceous energy sources.Ohara-Nemoto Y, Shimoyama Y, Kimura S, Kon A, Haraga H, Ono T, Nemoto TKJ Biol Chem10.1074/jbc.M111.2785722011Amino Acid Sequence, Aspartic Acid/*chemistry, Base Sequence, Cloning, Molecular, Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/chemistry/*metabolism, Gene Expression Regulation, Bacterial, Glutamic Acid/*chemistry, Humans, Hydrogen-Ion Concentration, Molecular Sequence Data, Polymerase Chain Reaction, Porphyromonas gingivalis/*enzymology, Protein Structure, Tertiary, Proteins/metabolism, Recombinant Proteins/chemistry, Sequence Homology, Amino AcidMetabolism
Phylogeny25494328Identification of Dipeptidyl-Peptidase (DPP)5 and DPP7 in Porphyromonas endodontalis, Distinct from Those in Porphyromonas gingivalis.Nishimata H, Ohara-Nemoto Y, Baba TT, Hoshino T, Fujiwara T, Shimoyama Y, Kimura S, Nemoto TKPLoS One10.1371/journal.pone.01142212014Amino Acid Sequence, Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/chemistry/*metabolism, Enzyme-Linked Immunosorbent Assay, Isoenzymes/chemistry/*metabolism, Porphyromonas/classification/*enzymology, Sequence Homology, Amino Acid, Species SpecificityMetabolism
Proteome27978916[Analysis of virulence factors of Porphyromonas endodontalis based on comparative proteomics technique].Li H, Ji H, Wu SS, Hou BXZhonghua Kou Qiang Yi Xue Za Zhi10.3760/cma.j.issn.1002-0098.2016.12.0092016Lipoproteins, *Porphyromonas endodontalis, Porphyromonas gingivalis, Proteomics, Tandem Mass Spectrometry, Virulence, Virulence Factors
Pathogenicity29308508[Antimicrobial effect of a new bio-ceramic material iRoot FM on Porphyromonas endodontalis].Bi J, Liu Y, Chen XShanghai Kou Qiang Yi Xue2017*Anti-Bacterial Agents/pharmacology, *Anti-Infective Agents/pharmacology, Calcium Hydroxide, Ceramics, Dental Prosthesis, *Porphyromonas endodontalis/drug effects

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17688Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24491)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24491
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
46485Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 16442)https://www.ccug.se/strain?id=16442
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
81728Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45021.1StrainInfo: A central database for resolving microbial strain identifiers