Strain identifier
BacDive ID: 12512
Type strain:
Species: Porphyromonas somerae
Strain history: CCUG 51464 <-- S. M. Finegold WAL 6690.
NCBI tax ID(s): 1122975 (strain), 322095 (species)
General
@ref: 16821
BacDive-ID: 12512
DSM-Number: 23386
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Porphyromonas somerae DSM 23386 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human leg ulcer.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1122975 | strain |
322095 | species |
strain history
@ref | history |
---|---|
16821 | <- CCUG <- S. M. Finegold, Dept. Veteran Affairs Medical Center, Los Angeles, USA; WAL 6690 |
67770 | CCUG 51464 <-- S. M. Finegold WAL 6690. |
doi: 10.13145/bacdive12512.20230509.8.1
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 somerae
- full scientific name: Porphyromonas somerae Summanen et al. 2006
@ref: 16821
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Porphyromonadaceae
genus: Porphyromonas
species: Porphyromonas somerae
full scientific name: Porphyromonas somerae Summanen et al. 2006 emend. Hahnke et al. 2016
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 100
colony morphology
@ref | type of hemolysis | hemolysis ability | incubation period |
---|---|---|---|
16821 | alpha/beta | 1 | |
59198 | 4 days |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16821 | 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 Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) Yeast extract 5.0 g/l K2HPO4 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 |
16821 | FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) | yes | https://mediadive.dsmz.de/medium/1203 | Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16821 | positive | growth | 37 | mesophilic |
59198 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
16821 | anaerobe | |
59198 | anaerobe | |
69480 | anaerobe | 99.162 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 98 |
69480 | no | 100 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68367 | 27082 | trehalose | - | builds acid from |
68367 | 62345 | L-rhamnose | - | builds acid from |
68367 | 30911 | sorbitol | - | builds acid from |
68367 | 16634 | raffinose | - | builds acid from |
68367 | 6731 | melezitose | - | builds acid from |
68367 | 16024 | D-mannose | + | builds acid from |
68367 | 17057 | cellobiose | - | builds acid from |
68367 | 17754 | glycerol | - | builds acid from |
68367 | 4853 | esculin | - | hydrolysis |
68367 | 5291 | gelatin | + | hydrolysis |
68367 | 30849 | L-arabinose | - | builds acid from |
68367 | 65327 | D-xylose | - | builds acid from |
68367 | 17814 | salicin | - | builds acid from |
68367 | 17306 | maltose | - | builds acid from |
68367 | 17992 | sucrose | - | builds acid from |
68367 | 17716 | lactose | + | builds acid from |
68367 | 16899 | D-mannitol | - | builds acid from |
68367 | 17634 | D-glucose | + | builds acid from |
68367 | 16199 | urea | - | hydrolysis |
68367 | 27897 | tryptophan | - | energy source |
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 | Chebi-ID | metabolite | production |
---|---|---|---|
68367 | 35581 | indole | no |
68380 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test |
---|---|---|---|
68380 | 35581 | indole | - |
68367 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
16821 | catalase | - | 1.11.1.6 |
16821 | cytochrome-c oxidase | - | 1.9.3.1 |
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate 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 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | + | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
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 | + | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
68367 | catalase | - | 1.11.1.6 |
68367 | beta-glucosidase | - | 3.2.1.21 |
68367 | gelatinase | + | |
68367 | urease | - | 3.5.1.5 |
API 20A
@ref | IND | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE | CAT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16821 | - | - | + | - | + | - | - | - | - | - | + | - | - | - | + | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16821 | - | - | - | + | +/- | - | - | - | - | + | - | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | + | - |
16821 | - | - | - | + | +/- | - | - | - | - | + | - | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | sampling date | geographic location |
---|---|---|---|---|---|---|
16821 | human leg ulcer | USA | USA | North America | ||
59198 | Human leg ulcer | USA | USA | North America | 1982-01-12 | Los Angeles |
67770 | Human leg ulcer |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body-Site | #Limb | #Leg |
#Infection | #Patient | |
#Host Body-Site | #Other | #Abscess |
taxonmaps
- @ref: 69479
- File name: preview.99_7462.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15883;96_3486;97_4273;98_5469;99_7462&stattab=map
- Last taxonomy: Porphyromonas somerae subclade
- 16S sequence: AB547667
- Sequence Identity:
- Total samples: 36106
- soil counts: 771
- aquatic counts: 822
- animal counts: 34358
- plant counts: 155
Safety information
risk assessment
- @ref: 16821
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Porphyromonas somerae gene for 16S ribosomal RNA, partial sequence, strain: JCM 13867 | AB547667 | 1486 | ena | 1122975 |
16821 | Porphyromonas somerae 16S ribosomal RNA gene, partial sequence | AY968205 | 1466 | ena | 1122975 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Porphyromonas somerae DSM 23386 | 1122975.3 | wgs | patric | 1122975 |
66792 | Porphyromonas somerae DSM 23386 | 2515154109 | draft | img | 1122975 |
67770 | Porphyromonas somerae DSM 23386 | GCA_000372405 | contig | ncbi | 1122975 |
GC content
- @ref: 16821
- GC-content: 47.1
- method: sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 98 | no |
motile | no | 91.953 | no |
flagellated | no | 97.203 | no |
gram-positive | no | 95.872 | no |
anaerobic | yes | 99.347 | yes |
aerobic | no | 98.439 | yes |
halophile | no | 87.139 | no |
spore-forming | no | 96.308 | no |
thermophile | no | 94.39 | no |
glucose-util | yes | 85.929 | no |
glucose-ferment | yes | 54.447 | no |
External links
@ref: 16821
culture collection no.: DSM 23386, ATCC BAA 1230, CCUG 51464, JCM 13867, WAL 6690
straininfo link
- @ref: 81731
- straininfo: 291135
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16821 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23386) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23386 | |||
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 | |
59198 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 51464) | https://www.ccug.se/strain?id=51464 | |||
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/ | ||||
68367 | Automatically annotated from API 20A | |||||
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 | |||
81731 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID291135.1 | StrainInfo: A central database for resolving microbial strain identifiers |