Strain identifier

BacDive ID: 130975

Type strain: Yes

Species: Bacteroides timonensis

Strain Designation: AP1

Strain history: <- J.-C. Lagier, Timone Hospital, Marseille, France; AP1 <- A. Pfleiderer

NCBI tax ID(s): 1470345 (species)

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General

@ref: 22267

BacDive-ID: 130975

DSM-Number: 26083

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

description: Bacteroides timonensis AP1 is an anaerobe, mesophilic bacterium that was isolated from human feces.

NCBI tax id

  • NCBI tax id: 1470345
  • Matching level: species

strain history

  • @ref: 22267
  • history: <- J.-C. Lagier, Timone Hospital, Marseille, France; AP1 <- A. Pfleiderer

doi: 10.13145/bacdive130975.20230509.8.1

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 timonensis
  • full scientific name: Bacteroides timonensis Ramasamy et al. 2014

@ref: 22267

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Clostridiales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides timonensis

full scientific name: Bacteroides timonensis

strain designation: AP1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.514
6948099.998negative

colony morphology

  • @ref: 22267
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22267COLUMBIA 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
22267CHOPPED 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

culture temp

  • @ref: 22267
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
22267anaerobe
69480anaerobe99.569

spore formation

@refspore formationconfidence
69481no100
69480no99.959

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

metabolite production

  • @ref: 68367
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 68367
  • 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
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 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
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
22267+-+-+++-++-+--+-+---

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
22267--++-++++/-+++++-++--+----+--+-
22267--++-+++-+++++/--+/-+--+----+--+-

Isolation, sampling and environmental information

isolation

  • @ref: 22267
  • sample type: human feces
  • country: France
  • origin.country: FRA
  • continent: Europe
  • latitude: 43.2965
  • longitude: 5.3697

isolation source categories

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

Sequence information

16S sequences

  • @ref: 22267
  • description: Bacteroides timonensis AP1 16S ribosomal RNA gene, partial sequence
  • accession: JX041639
  • length: 1315
  • database: ena
  • NCBI tax ID: 1203465

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides timonensis AP1GCA_000513195contigncbi1470345
66792Bacteroides timonensis AP12600255085draftimg1203465

GC content

  • @ref: 22267
  • GC-content: 43.3
  • method: sequence analysis

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 100
  • training_data: no

External links

@ref: 22267

culture collection no.: DSM 26083, CSUR P194

literature

  • topic: Genetics
  • Pubmed-ID: 25197491
  • title: Genome sequence and description of Bacteroides timonensis sp. nov.
  • authors: Ramasamy D, Lagier JC, Rossi-Tamisier M, Pfleiderer A, Michelle C, Couderc C, Raoult D, Fournier PE
  • journal: Stand Genomic Sci
  • DOI: 10.4056/sigs.5389564
  • year: 2014
  • topic2: Phylogeny

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
22267Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26083Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26083)
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
68367Automatically annotated from API 20A
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1