Strain identifier

BacDive ID: 12513

Type strain: Yes

Species: Porphyromonas bennonis

Strain history: CCUG 55979 <-- S. M. Finegold WAL 1926C.

NCBI tax ID(s): 1122971 (strain), 501496 (species)

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General

@ref: 16681

BacDive-ID: 12513

DSM-Number: 23058

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped

description: Porphyromonas bennonis DSM 23058 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human spontaneous shoulder abscess .

NCBI tax id

NCBI tax idMatching level
501496species
1122971strain

strain history

@refhistory
16681<- CCUG <- S. M. Finegold, Los Angeles, USA
67770CCUG 55979 <-- S. M. Finegold WAL 1926C.

doi: 10.13145/bacdive12513.20230509.8.1

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 bennonis
  • full scientific name: Porphyromonas bennonis Summanen et al. 2009

@ref: 16681

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Porphyromonadaceae

genus: Porphyromonas

species: Porphyromonas bennonis

full scientific name: Porphyromonas bennonis Summanen et al. 2009 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28930negative3.5 µm0.85 µmrod-shaped
69480no90.595
69480negative99.999

colony morphology

@reftype of hemolysisincubation period
16681gamma
608134 days

pigmentation

  • @ref: 28930
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16681COLUMBIA 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
16681CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) Composition: Ground beef 500.0 g/l Horse serum 50.0 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 (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

culture temp

@refgrowthtypetemperaturerange
16681positivegrowth37mesophilic
60813positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16681anaerobe
28930anaerobe
60813anaerobe
69480anaerobe99.289

spore formation

@refspore formationconfidence
28930no
69481no100
69480no99.998

observation

  • @ref: 28930
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2893030089acetate+carbon source
289305291gelatin+carbon source
2893030031succinate+carbon source
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose-builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
16681catalase+1.11.1.6
16681cytochrome-c oxidase-1.9.3.1
28930catalase+1.11.1.6
68380serine arylamidase-
68380glutamyl-glutamate 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
68380N-acetyl-beta-glucosaminidase+3.2.1.52
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+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
16681--------------------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16681---++/-+---+------+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16681human spontaneous shoulder abscess (diabetes mellitus)Los AngelesUSAUSANorth America
60813Human shoulder abscessLos AngelesUSAUSANorth America2007-06-25
67770Human clinical specimen

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Other#Abscess
#Host Body-Site#Limb#Arm

Safety information

risk assessment

  • @ref: 16681
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16681Porphyromonas bennonis strain WAL 1926C 16S ribosomal RNA gene, partial sequenceEU4146731489ena501496
67770Porphyromonas bennonis gene for 16S ribosomal RNA, partial sequence, strain: JCM 16335AB5880201498ena501496

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Porphyromonas bennonis DSM 230581122971.3wgspatric1122971
66792Porphyromonas bennonis JCM 163351236537.5wgspatric1122971
66792Porphyromonas bennonis JCM 163352585427886draftimg1122971
66792Porphyromonas bennonis DSM 230582517093003draftimg1122971
67770Porphyromonas bennonis DSM 23058 = JCM 16335GCA_000375645contigncbi1122971
67770Porphyromonas bennonis DSM 23058 = JCM 16335GCA_000615615contigncbi1122971

GC content

@refGC-contentmethod
1668158.0high performance liquid chromatography (HPLC)
1668156.3sequence analysis
6777058high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.84no
flagellatedno97.556no
gram-positiveno94.838yes
anaerobicyes98.193yes
aerobicno97.633yes
halophileno86.375no
spore-formingno97.498yes
glucose-utilyes85.725no
thermophileno97.594yes
glucose-fermentyes57.77no

External links

@ref: 16681

culture collection no.: DSM 23058, ATCC BAA 1629, CCUG 55979, WAL 1926C, JCM 16335

straininfo link

  • @ref: 81732
  • straininfo: 399894

literature

  • topic: Phylogeny
  • Pubmed-ID: 19542133
  • title: Porphyromonas bennonis sp. nov., isolated from human clinical specimens.
  • authors: Summanen PH, Lawson PA, Finegold SM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.001909-0
  • year: 2009
  • mesh: Bacterial Typing Techniques, Bacteroidaceae Infections/*microbiology, DNA, Bacterial/analysis, Genes, rRNA, Genotype, Humans, Molecular Sequence Data, Phenotype, Phylogeny, Porphyromonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16681Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23058)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23058
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
28930Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2536928776041
60813Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55979)https://www.ccug.se/strain?id=55979
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
81732Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399894.1StrainInfo: A central database for resolving microbial strain identifiers