Strain identifier

BacDive ID: 1594

Type strain: Yes

Species: Bacteroides pyogenes

Strain Designation: P39-88

Strain history: Y. Benno P39-88.

NCBI tax ID(s): 1121100 (strain), 310300 (species)

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General

@ref: 8959

BacDive-ID: 1594

DSM-Number: 20611

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, animal pathogen

description: Bacteroides pyogenes P39-88 is an anaerobe, mesophilic animal pathogen that was isolated from pig faeces.

NCBI tax id

NCBI tax idMatching level
310300species
1121100strain

strain history

@refhistory
8959<- Y. Benno, P39-88
67770Y. Benno P39-88.

doi: 10.13145/bacdive1594.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Bacteroidaceae
  • genus: Bacteroides
  • species: Bacteroides pyogenes
  • full scientific name: Bacteroides pyogenes Benno et al. 1983

  • synonyms

    @refsynonym
    20215Bacteroides tectus
    20215Bacteroides tectum
    20215Bacteroides suis

@ref: 8959

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides pyogenes

full scientific name: Bacteroides pyogenes Benno et al. 1983 emend. Sakamoto et al. 2010

strain designation: P39-88

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.165
6948099.967negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8959CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: 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
8959PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
8959positivegrowth37mesophilic
46249positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8959anaerobe
46249anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481no95
69480no99.999

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine 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 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46249C15:03.215
    46249C16:03.416
    46249C17:00.417
    46249C18:0118
    46249C13:0 ANTEISO0.412.701
    46249C13:0 iso0.412.612
    46249C15:0 3OH1.116.504
    46249C15:0 ANTEISO27.614.711
    46249C15:0 ISO16.314.621
    46249C16:0 3OH2.317.52
    46249C16:0 iso1.315.626
    46249C16:1 ω7c0.415.819
    46249C17:0 2OH1.618.249
    46249C17:0 3OH1.218.535
    46249C17:0 anteiso616.722
    46249C17:0 iso3.716.629
    46249C17:0 iso 3OH14.618.161
    46249C18:1 ω9c317.769
    46249C18:2 ω6,9c/C18:0 ANTE4.817.724
    46249Unidentified0.516.123
    46249unknown 13.5666.513.566
    46249unknown 16.5800.416.58
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8959---+-+---++--+--+--+----+--+/--

Isolation, sampling and environmental information

isolation

@refsample type
8959pig faeces
46249Pig abscess (formerly listed as:pig feces)
67770Pig abscess

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1244.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_206;96_722;97_845;98_984;99_1244&stattab=map
  • Last taxonomy: Bacteroides pyogenes subclade
  • 16S sequence: AB542768
  • Sequence Identity:
  • Total samples: 38767
  • soil counts: 529
  • aquatic counts: 520
  • animal counts: 37576
  • plant counts: 142

Safety information

risk assessment

  • @ref: 8959
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides pyogenes gene for 16S ribosomal RNA, partial sequence, strain: ATCC 35418AB5427661478ena310300
20218Bacteroides pyogenes gene for 16S ribosomal RNA, partial sequence, strain: DSM 20611AB5427681476ena310300
8959Bacteroides pyogenes strain JCM6294 16S ribosomal RNA gene, partial sequenceEU1366832063ena310300
67770Bacteroides pyogenes gene for 16S rRNA, partial sequence, strain: JCM 6294AB2002291461ena310300
67770Bacteroides pyogenes gene for 16S ribosomal RNA, partial sequence, strain: CCUG 15419AB5427671477ena310300

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides pyogenes DSM 20611 = JCM 6294GCA_000428105scaffoldncbi1121100
66792Bacteroides pyogenes DSM 206111121100.7wgspatric1121100
66792Bacteroides pyogenes JCM 62941235810.3wgspatric1121100
66792Bacteroides pyogenes DSM 206112524614554draftimg1121100
66792Bacteroides pyogenes JCM 62942574180081draftimg1121100
67770Bacteroides pyogenes DSM 20611 = JCM 6294GCA_000511755contigncbi1121100

GC content

@refGC-contentmethod
895946.7
6777046.8thermal denaturation, midpoint method (Tm)
6777046.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileno93.015no
flagellatedno97.898no
gram-positiveno96.623no
anaerobicyes99.202no
aerobicno97.941yes
halophileno93.718no
spore-formingno95.014no
glucose-utilyes88.776no
thermophileno95.966no
glucose-fermentyes69.455no

External links

@ref: 8959

culture collection no.: DSM 20611, ATCC 35418, CCUG 15419, JCM 6294

straininfo link

  • @ref: 71239
  • straininfo: 41066

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20118288hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes.Sakamoto M, Suzuki N, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.021154-02010Bacteroides/*classification, Chaperonin 60/*genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Genetics24482517Draft Genome Sequences of Three Strains of Bacteroides pyogenes Isolated from a Cat and Swine.Sakamoto M, Oshima K, Suda W, Kitamura K, Iida T, Hattori M, Ohkuma MGenome Announc10.1128/genomeA.01242-132014Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8959Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20611)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20611
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
46249Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15419)https://www.ccug.se/strain?id=15419
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/
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
71239Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41066.1StrainInfo: A central database for resolving microbial strain identifiers