Strain identifier

BacDive ID: 159554

Type strain: No

Species: Gordonibacter pamelaeae

Strain Designation: 3C

Strain history: <- J. Bisanz and P. J. Turnbaugh, University of California, San Francisco, USA;

NCBI tax ID(s): 471189 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 9.1 (current version)

General

@ref: 66380

BacDive-ID: 159554

DSM-Number: 110924

keywords: genome sequence, Bacteria, anaerobe, human pathogen

description: Gordonibacter pamelaeae 3C is an anaerobe human pathogen that was isolated from feces, human.

NCBI tax id

  • NCBI tax id: 471189
  • Matching level: species

strain history

  • @ref: 66380
  • history: <- J. Bisanz and P. J. Turnbaugh, University of California, San Francisco, USA;

doi: 10.13145/bacdive159554.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Eggerthellales
  • family: Eggerthellaceae
  • genus: Gordonibacter
  • species: Gordonibacter pamelaeae
  • full scientific name: Gordonibacter pamelaeae Würdemann et al. 2009

@ref: 66380

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Eggerthellales

family: Eggerthellaceae

genus: Gordonibacter

species: Gordonibacter pamelaeae

full scientific name: Gordonibacter pamelaeae Würdemann et al. 2009 emend. Jin et al. 2014

strain designation: 3C

type strain: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
66380BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215; with strain-specific modifications) Composition: Brain heart infusion 37.0 g/l Arginine 10.0 g/l Distilled water
66380COLUMBIA 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

culture temp

  • @ref: 66380
  • growth: positive
  • type: growth
  • temperature: 37

Physiology and metabolism

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
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 rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
66380-+----------+----------------

Isolation, sampling and environmental information

isolation

  • @ref: 66380
  • sample type: feces, human
  • geographic location: Cambridge, Massachusetts
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human

Safety information

risk assessment

  • @ref: 66380
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

  • @ref: 66792
  • description: Gordonibacter pamelaeae 3C
  • accession: GCA_003340385
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 471189

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes78.548no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes87.744no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.113no
69480spore-formingspore-formingAbility to form endo- or exosporesno73.182no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno91.499yes
69480flagellatedmotile2+Ability to perform flagellated movementno79.5no

External links

@ref: 66380

culture collection no.: DSM 110924

straininfo link

  • @ref: 112033
  • straininfo: 397471

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
66380Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-110924Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 110924)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68380Automatically annotated from API rID32A
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
112033Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID397471.1