Strain identifier

BacDive ID: 1595

Type strain: No

Species: Bacteroides pyogenes

Strain Designation: P 38024

Strain history: Y. Benno P38024 <-- T. Mitsuoka.

NCBI tax ID(s): 1235809 (strain), 310300 (species)

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General

@ref: 8960

BacDive-ID: 1595

DSM-Number: 20612

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

description: Bacteroides pyogenes P 38024 is an anaerobe, mesophilic animal pathogen that was isolated from pig faeces.

NCBI tax id

NCBI tax idMatching level
1235809strain
310300species

strain history

@refhistory
8960<- Y. Benno, P 38024
67770Y. Benno P38024 <-- T. Mitsuoka.

doi: 10.13145/bacdive1595.20230509.8.1

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: 8960

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: P 38024

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.961
6948099.976negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8960CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
8960PYG 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
8960positivegrowth37mesophilic
46250positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8960anaerobe
46250anaerobe
69480anaerobe99.633

spore formation

@refspore formationconfidence
69481no100
69480no99.999

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
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
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
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 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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
46250-+--------++---+-+--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
46250---+-+---+---+--+--+----+--+-
8960---+-+---+++-+--+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample type
8960pig faeces
46250Pig feces
67770Pig feces

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: AB510709
  • Sequence Identity:
  • Total samples: 38767
  • soil counts: 529
  • aquatic counts: 520
  • animal counts: 37576
  • plant counts: 142

Safety information

risk assessment

  • @ref: 8960
  • 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 35419AB5427691490ena310300
20218Bacteroides pyogenes gene for 16S ribosomal RNA, partial sequence, strain: DSM 20612AB5427711476ena310300
67770Bacteroides pyogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 6292AB5107091490ena310300
67770Bacteroides pyogenes gene for 16S ribosomal RNA, partial sequence, strain: CCUG 15420AB5427701477ena310300

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides pyogenes JCM 62921235809.3wgspatric1235809
66792Bacteroides pyogenes JCM 62922576861690draftimg1235809
67770Bacteroides pyogenes JCM 6292GCA_000511735contigncbi1235809

GC content

@refGC-contentmethod
896044.2
6777042.6thermal denaturation, midpoint method (Tm)
6777046.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.882no
gram-positiveno97.276no
anaerobicyes99.168yes
aerobicno98.161yes
halophileno93.952no
spore-formingno95.09no
glucose-utilyes89.191no
flagellatedno97.801no
thermophileno96.084yes
glucose-fermentyes64.926no

External links

@ref: 8960

culture collection no.: CCUG 15420, CCM 3725, DSM 20612, ATCC 35419, JCM 6292

straininfo link

  • @ref: 71240
  • straininfo: 41067

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8960Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20612)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20612
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
46250Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15420)https://www.ccug.se/strain?id=15420
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
68382Automatically annotated from API zym
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
71240Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41067.1StrainInfo: A central database for resolving microbial strain identifiers