Strain identifier
BacDive ID: 162568
Type strain: 
Species: Porphyromonas gingivalis
Strain history: I. Nakagawa TDC60 <-- Tokyo Dent. Coll..
NCBI tax ID(s): 837 (species)
version 8.1 (current version)
General
@ref: 67770
BacDive-ID: 162568
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Porphyromonas gingivalis JCM 19600 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from Severe periodontal lesion.
NCBI tax id
- NCBI tax id: 837
- Matching level: species
strain history
- @ref: 67770
- history: I. Nakagawa TDC60 <-- Tokyo Dent. Coll..
doi: 10.13145/bacdive162568.20230509.8.1
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 gingivalis
- full scientific name: Porphyromonas gingivalis (Coykendall et al. 1980) Shah and Collins 1988
synonyms
- @ref: 20215
- synonym: Bacteroides gingivalis
@ref: 67770
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
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.971
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: anaerobe
- confidence: 99.603
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 99.997 |
| 69481 | no | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Severe periodontal lesion
taxonmaps
- @ref: 69479
- File name: preview.99_847.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15851;96_508;97_586;98_673;99_847&stattab=map
- Last taxonomy: Porphyromonas gingivalis subclade
- 16S sequence: AB910743
- Sequence Identity:
- Total samples: 35027
- soil counts: 1092
- aquatic counts: 1398
- animal counts: 32086
- plant counts: 451
Sequence information
16S sequences
- @ref: 67770
- description: Porphyromonas gingivalis gene for 16S ribosomal RNA, partial sequence
- accession: AB910743
- length: 1493
- database: ena
- NCBI tax ID: 837
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Porphyromonas gingivalis strain TDC 60 | 837.133 | complete | patric | 837 |
| 67770 | Porphyromonas gingivalis TDC60 | GCA_000270225 | complete | ncbi | 1030843 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 91.442 | no |
| flagellated | no | 96.708 | no |
| gram-positive | no | 96.866 | no |
| anaerobic | yes | 99.368 | no |
| halophile | no | 80.546 | no |
| spore-forming | no | 95.917 | no |
| thermophile | no | 97.753 | no |
| glucose-util | yes | 81.589 | no |
| aerobic | no | 98.53 | no |
| glucose-ferment | no | 52.143 | no |
External links
@ref: 67770
culture collection no.: JCM 19600
literature
- Pubmed-ID: 31137477
- title: In Vitro Effect of the Traditional Medicine Hainosan (Painongsan) on Porphyromonas gingivalis.
- authors: Minami M, Takase H, Taira M, Makino T
- journal: Medicines (Basel)
- DOI: 10.3390/medicines6020058
- year: 2019
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 69479 | João 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 beta | https://microbeatlas.org/ |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |