Strain identifier
BacDive ID: 12505
Type strain:
Species: Porphyromonas asaccharolytica
Strain Designation: B440
Strain history: ATCC 25260 <-- W. E. C. Moore VPI 4198 <-- S. Finegold B440.
NCBI tax ID(s): 879243 (strain), 28123 (species)
General
@ref: 8784
BacDive-ID: 12505
DSM-Number: 20707
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, rod-shaped, human pathogen
description: Porphyromonas asaccharolytica B440 is an anaerobe, mesophilic, rod-shaped human pathogen that was isolated from empyema.
NCBI tax id
NCBI tax id | Matching level |
---|---|
28123 | species |
879243 | strain |
strain history
@ref | history |
---|---|
8784 | <- ATCC <- W.E.C. Moore, VPI 4198 (Bacteroides melaninogenicus subsp. asaccharolyticus) <- S. Finegold, B440 |
67770 | ATCC 25260 <-- W. E. C. Moore VPI 4198 <-- S. Finegold B440. |
doi: 10.13145/bacdive12505.20230509.8.1
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 asaccharolytica
- full scientific name: Porphyromonas asaccharolytica (Holdeman and Moore 1970) Shah and Collins 1988
synonyms
@ref synonym 20215 Bacteroides melaninogenicus subsp. asaccharolyticus 20215 Bacteroides asaccharolyticus
@ref: 8784
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Porphyromonadaceae
genus: Porphyromonas
species: Porphyromonas asaccharolytica
full scientific name: Porphyromonas asaccharolytica (Holdeman and Moore 1970) Shah and Collins 1988 emend. Hahnke et al. 2016
strain designation: B440
type strain: yes
Morphology
cell morphology
@ref | cell shape | gram stain | motility | confidence |
---|---|---|---|---|
68367 | rod-shaped | |||
68367 | negative | |||
69480 | no | 92.044 | ||
69480 | negative | 99.997 |
colony morphology
- @ref: 45041
- incubation period: 3 days
multimedia
- @ref: 66793
- multimedia content: EM_DSM_20707_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8784 | 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 |
8784 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 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 (optional) 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 |
---|---|---|---|---|
8784 | positive | growth | 37 | mesophilic |
45041 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
8784 | anaerobe | |
45041 | anaerobe | |
69480 | anaerobe | 99.531 |
spore formation
@ref | spore formation | confidence |
---|---|---|
68367 | no | |
69481 | no | 100 |
69480 | no | 99.998 |
observation
- @ref: 67770
- observation: quinones: MK-10, MK-11, MK-9
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 | 4853 | esculin | - | hydrolysis |
68367 | 5291 | gelatin | + | hydrolysis |
68367 | 30849 | L-arabinose | - | builds acid from |
68367 | 65327 | D-xylose | - | 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 | 16199 | urea | - | hydrolysis |
68367 | 27897 | tryptophan | + | energy source |
68380 | 16199 | urea | - | hydrolysis |
68380 | 16024 | D-mannose | - | 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 | yes |
68380 | 35581 | indole | yes |
metabolite tests
@ref | Chebi-ID | metabolite | indole test |
---|---|---|---|
68380 | 35581 | indole | + |
68367 | 35581 | indole | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
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 | 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 | SPOR | GRAM | COCC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8784 | + | - | +/- | - | - | - | - | +/- | - | - | + | - | +/- | - | - | - | - | - | - | - | - | - | - | - |
8784 | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8784 | - | - | - | - | - | - | - | - | - | - | - | + | - | + | - | + | + | - | - | + | - | - | - | +/- | + | - | - | +/- | - |
8784 | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | + | - | - | + | - | +/- | - | - | + | - | - | +/- | - |
8784 | - | + | - | - | - | - | - | - | - | - | - | - | - | + | - | + | + | +/- | - | + | - | + | - | - | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
8784 | empyema |
45041 | Human empyema |
67770 | Empyema |
isolation source categories
- Cat1: #Host Body Product
- Cat2: #Fluids
taxonmaps
- @ref: 69479
- File name: preview.99_3456.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_391;96_1725;97_2066;98_2541;99_3456&stattab=map
- Last taxonomy: Porphyromonas asaccharolytica
- 16S sequence: NR_074588
- Sequence Identity:
- Total samples: 14984
- soil counts: 179
- aquatic counts: 178
- animal counts: 14606
- plant counts: 21
Safety information
risk assessment
- @ref: 8784
- pathogenicity human: yes
- pathogenicity animal: yes
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Porphyromonas asaccharolytica strain ATCC 25260 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequence | AF386069 | 672 | ena | 879243 |
20218 | Porphyromonas asaccharolytica strain ATCC 25260 16S-23S ribosomal RNA intergenic spacer, partial sequence | AY546484 | 858 | ena | 879243 |
20218 | Porphyromonas asaccharolytica strain ATCC 25260 16S ribosomal RNA gene, partial sequence | FJ792537 | 1368 | ena | 879243 |
20218 | Porphyromonas asaccharolytica DSM 20707 strain ATCC 25260 16S ribosomal RNA gene, partial sequence | L16490 | 1478 | ena | 879243 |
8784 | Porphyromonas asaccharolytica DSM 20707 16S ribosomal RNA, partial sequence | NR_074588 | 1517 | nuccore | 879243 |
67770 | Porphyromonas asaccharolytica gene for 16S ribosomal RNA, partial sequence, strain: JCM 6326 | AB547653 | 1479 | ena | 879243 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Porphyromonas asaccharolytica DSM 20707 | GCA_000212375 | complete | ncbi | 879243 |
66792 | Porphyromonas asaccharolytica DSM 20707 | 879243.3 | complete | patric | 879243 |
66792 | Porphyromonas asaccharolytica VPI 4198, DSM 20707 | 2504756018 | complete | img | 879243 |
GC content
@ref | GC-content | method |
---|---|---|
8784 | 52.1 | |
8784 | 52.5 | sequence analysis |
67770 | 53 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 89.322 | no |
flagellated | no | 97.264 | no |
gram-positive | no | 97.835 | no |
anaerobic | yes | 99.416 | no |
aerobic | no | 98.12 | yes |
halophile | no | 83.456 | no |
spore-forming | no | 96.788 | yes |
thermophile | no | 95.094 | no |
glucose-util | yes | 82.833 | no |
glucose-ferment | yes | 52.822 | no |
External links
@ref: 8784
culture collection no.: CCUG 7834, CCUG 14451, JCM 6326, DSM 20707, ATCC 25260, VPI 4198, BCRC 10618, LMG 13178
straininfo link
- @ref: 81724
- straininfo: 13933
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 7981094 | Porphyromonas gingivicanis sp. nov. and Porphyromonas crevioricanis sp. nov., isolated from beagles. | Hirasawa M, Takada K | Int J Syst Bacteriol | 10.1099/00207713-44-4-637 | 1994 | Animals, DNA, Bacterial/analysis, Dogs/*microbiology, Gingiva/microbiology, Porphyromonas/genetics/*isolation & purification/metabolism | Enzymology |
Phylogeny | 8186085 | Porphyromonas 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 H | Int J Syst Bacteriol | 10.1099/00207713-44-2-204 | 1994 | Animals, 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 & purification | Metabolism |
9871324 | Phospholipid molecular species distribution of Porphyromonas asaccharolytica ATCC 25260T: effects of temperature, culture age and pH. | Tavana AM, Drucker DB, Boote V | J Appl Microbiol | 10.1111/j.1365-2672.1998.tb05268.x | 1998 | Hydrogen-Ion Concentration, Phospholipids/*analysis, Porphyromonas/*chemistry, Temperature | ||
Phylogeny | 15774632 | 16S-23S rRNA gene internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Porphyromonas. | Conrads G, Citron DM, Tyrrell KL, Horz HP, Goldstein EJC | Int J Syst Evol Microbiol | 10.1099/ijs.0.63234-0 | 2005 | Bacterial Typing Techniques, DNA, Ribosomal Spacer/*analysis, Genes, rRNA, Humans, Molecular Sequence Data, *Phylogeny, Porphyromonas/*classification/genetics, RNA, Ribosomal, 16S/*genetics, RNA, Ribosomal, 23S/*genetics, Sequence Analysis, DNA, Species Specificity | Transcriptome |
35618163 | Chalcones with potential antibacterial and antibiofilm activities against periodontopathogenic bacteria. | Satokata AAC, Souza JH, Silva LLO, Santiago MB, Ramos SB, Assis LR, Theodoro RDS, Oliveira LRE, Regasini LO, Martins CHG | Anaerobe | 10.1016/j.anaerobe.2022.102588 | 2022 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8784 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20707) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20707 | |||
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 | |
45041 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 7834) | https://www.ccug.se/strain?id=7834 | |||
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) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
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 | |||
81724 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13933.1 | StrainInfo: A central database for resolving microbial strain identifiers |