Strain identifier

BacDive ID: 1602

Type strain: No

Species: Phocaeicola vulgatus

Strain history: <- ATCC <- Wadsworth Anaerobic Bact. Res. Lab., WAL 1887

NCBI tax ID(s): 821 (species)

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General

@ref: 1346

BacDive-ID: 1602

DSM-Number: 3289

keywords: Bacteria, anaerobe, mesophilic, human pathogen

description: Phocaeicola vulgatus CCUG 12546 is an anaerobe, mesophilic human pathogen that was isolated from retroperitoneal abscess.

NCBI tax id

  • NCBI tax id: 821
  • Matching level: species

strain history

  • @ref: 1346
  • history: <- ATCC <- Wadsworth Anaerobic Bact. Res. Lab., WAL 1887

doi: 10.13145/bacdive1602.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Bacteroidaceae
  • genus: Phocaeicola
  • species: Phocaeicola vulgatus
  • full scientific name: Phocaeicola vulgatus (Eggerth and Gagnon 1933) García-López et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Bacteroides vulgatus

@ref: 1346

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Phocaeicola

species: Phocaeicola vulgatus

full scientific name: Phocaeicola vulgatus (Eggerth and Gagnon 1933) García-López et al. 2020

type strain: no

Culture and growth conditions

culture medium

  • @ref: 1346
  • name: CHOPPED MEAT MEDIUM (DSMZ Medium 78)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/78
  • composition: 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: 1346
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 1346
  • oxygen tolerance: anaerobe

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-
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
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
45742--++-+-+-+++-+--+--+----++-+-
1346--+++/-+-++/-+++-+--+--+----++-+-
1346--+++/-+-++/-+++-+--+--+----++-+-

Isolation, sampling and environmental information

isolation

@refsample type
1346retroperitoneal abscess
45742Human retroperitoneal abscess

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Other#Abdomen
#Host Body-Site#Other#Abscess

Safety information

risk assessment

  • @ref: 1346
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

External links

@ref: 1346

culture collection no.: CCUG 12546, KCTC 2639, DSM 3289, ATCC 29327, WAL 1887

straininfo link

  • @ref: 71247
  • straininfo: 39470

literature

  • topic: Pathogenicity
  • Pubmed-ID: 3972999
  • title: Evaluation of broth microdilution susceptibility results for anaerobic organisms by use of a rapid direct colony inoculum.
  • authors: Mangels JI, Lindberg LH
  • journal: J Clin Microbiol
  • DOI: 10.1128/jcm.21.2.269-272.1985
  • year: 1985
  • mesh: Bacteria, Anaerobic/*drug effects, Humans, Microbial Sensitivity Tests/*methods, Quality Control, Tetracycline/pharmacology

Reference

@idauthorscataloguedoi/urltitle
1346Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3289)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3289
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
45742Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12546)https://www.ccug.se/strain?id=12546
68380Automatically annotated from API rID32A
71247Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39470.1StrainInfo: A central database for resolving microbial strain identifiers