Strain identifier

BacDive ID: 12512

Type strain: Yes

Species: Porphyromonas somerae

Strain history: CCUG 51464 <-- S. M. Finegold WAL 6690.

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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 idMatching level
1122975strain
322095species

strain history

@refhistory
16821<- CCUG <- S. M. Finegold, Dept. Veteran Affairs Medical Center, Los Angeles, USA; WAL 6690
67770CCUG 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

@reftype of hemolysishemolysis abilityincubation period
16821alpha/beta1
591984 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16821CHOPPED 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 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
16821FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)yeshttps://mediadive.dsmz.de/medium/1203Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16821positivegrowth37mesophilic
59198positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16821anaerobe
59198anaerobe
69480anaerobe99.162

spore formation

@refspore formationconfidence
69481no98
69480no100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
16821catalase-1.11.1.6
16821cytochrome-c oxidase-1.9.3.1
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
68367catalase-1.11.1.6
68367beta-glucosidase-3.2.1.21
68367gelatinase+
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECAT
16821--+-+-----+---+------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16821---++/-----+------+--+----+--+-
16821---++/-----+------+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
16821human leg ulcerUSAUSANorth America
59198Human leg ulcerUSAUSANorth America1982-01-12Los Angeles
67770Human leg ulcer

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Porphyromonas somerae gene for 16S ribosomal RNA, partial sequence, strain: JCM 13867AB5476671486ena1122975
16821Porphyromonas somerae 16S ribosomal RNA gene, partial sequenceAY9682051466ena1122975

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Porphyromonas somerae DSM 233861122975.3wgspatric1122975
66792Porphyromonas somerae DSM 233862515154109draftimg1122975
67770Porphyromonas somerae DSM 23386GCA_000372405contigncbi1122975

GC content

  • @ref: 16821
  • GC-content: 47.1
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno91.953no
flagellatedno97.203no
gram-positiveno95.872no
anaerobicyes99.347yes
aerobicno98.439yes
halophileno87.139no
spore-formingno96.308no
thermophileno94.39no
glucose-utilyes85.929no
glucose-fermentyes54.447no

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

@idauthorscataloguedoi/urltitlejournalpubmed
16821Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23386)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23386
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
59198Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51464)https://www.ccug.se/strain?id=51464
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
69479João 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
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
81731Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID291135.1StrainInfo: A central database for resolving microbial strain identifiers