Strain identifier
BacDive ID: 12511
Type strain:
Species: Porphyromonas uenonis
Strain history: CCUG 48615 <-- S. M. Finegold WAL 9902.
NCBI tax ID(s): 1122976 (strain), 281920 (species)
General
@ref: 16823
BacDive-ID: 12511
DSM-Number: 23387
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Porphyromonas uenonis DSM 23387 is an anaerobe, mesophilic bacterium that was isolated from human sacral decubitus ulcer.
NCBI tax id
NCBI tax id | Matching level |
---|---|
281920 | species |
1122976 | strain |
strain history
@ref | history |
---|---|
16823 | <- CCUG <- S. M. Finegold, Dept. Veteran Affairs Medical Center, Los Angeles, USA <- Wadsworth Anaerobe Lab., Los Angeles, CA, USA |
67770 | CCUG 48615 <-- S. M. Finegold WAL 9902. |
doi: 10.13145/bacdive12511.20230509.8.1
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 uenonis
- full scientific name: Porphyromonas uenonis Finegold et al. 2005
@ref: 16823
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Porphyromonadaceae
genus: Porphyromonas
species: Porphyromonas uenonis
full scientific name: Porphyromonas uenonis Finegold et al. 2005
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 90.086 | |
69480 | 99.992 | negative |
colony morphology
- @ref: 58261
- incubation period: 2 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16823 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
16823 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) Composition: Ground beef 500.0 g/l Bovine serum 50.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16823 | positive | growth | 37 | mesophilic |
58261 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
16823 | anaerobe | |
58261 | anaerobe | |
69480 | anaerobe | 99.537 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.999 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | + | 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
@ref | value | activity | ec |
---|---|---|---|
16823 | catalase | - | 1.11.1.6 |
16823 | cytochrome-c oxidase | - | 1.9.3.1 |
68380 | serine arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | + | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | alkaline phosphatase | + | 3.1.3.1 |
68380 | tryptophan deaminase | + | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | - | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | - | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16823 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | - | - | - | - | + | - | - | + | - |
16823 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | +/- | - | + | - | +/- | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
16823 | human sacral decubitus ulcer | Los Angeles, CA | USA | USA | North America | |
58261 | Human sacral decubitus ulcer | 1991 | ||||
67770 | Human sacral decubitus ulcer |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body-Site | #Organ | #Skin, Nail, Hair |
taxonmaps
- @ref: 69479
- File name: preview.99_3315.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_391;96_1725;97_2066;98_2541;99_3315&stattab=map
- Last taxonomy: Porphyromonas uenonis
- 16S sequence: AB547668
- Sequence Identity:
- Total samples: 6885
- soil counts: 65
- aquatic counts: 50
- animal counts: 6767
- plant counts: 3
Safety information
risk assessment
- @ref: 16823
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Porphyromonas uenonis gene for 16S ribosomal RNA, partial sequence, strain: JCM 13868 | AB547668 | 1490 | ena | 281920 |
16823 | Porphyromonas uenonis 16S ribosomal RNA gene, partial sequence | AY570514 | 1457 | ena | 281920 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Porphyromonas uenonis DSM 23387 | 1122976.3 | wgs | patric | 1122976 |
66792 | Porphyromonas uenonis JCM 13868 | 1236493.3 | wgs | patric | 1122976 |
66792 | Porphyromonas uenonis JCM 13868 | 2585427891 | draft | img | 1122976 |
66792 | Porphyromonas uenonis DSM 23387 | 2528311143 | draft | img | 1122976 |
67770 | Porphyromonas uenonis DSM 23387 = JCM 13868 | GCA_000482365 | scaffold | ncbi | 1122976 |
67770 | Porphyromonas uenonis DSM 23387 = JCM 13868 | GCA_000613705 | contig | ncbi | 1122976 |
GC content
@ref | GC-content | method |
---|---|---|
16823 | 52.5 | |
67770 | 52.5 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 90.386 | no |
flagellated | no | 97.514 | no |
gram-positive | no | 97.333 | no |
anaerobic | yes | 99.3 | yes |
aerobic | no | 97.447 | yes |
halophile | no | 81.625 | no |
spore-forming | no | 96.707 | no |
thermophile | no | 95.755 | no |
glucose-util | yes | 79.884 | no |
glucose-ferment | yes | 51.654 | no |
External links
@ref: 16823
culture collection no.: DSM 23387, ATCC BAA 906, CCUG 48615, JCM 13868, WAL 9902
straininfo link
- @ref: 81730
- straininfo: 133438
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16823 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23387) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23387 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
58261 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 48615) | https://www.ccug.se/strain?id=48615 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68380 | Automatically annotated from API rID32A | |||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
81730 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID133438.1 | StrainInfo: A central database for resolving microbial strain identifiers |