Strain identifier

BacDive ID: 24536

Type strain: Yes

Species: Alistipes timonensis

Strain Designation: JC136

Strain history: DSM 25383 <-- J.-C. Lagier; Timone Hosp., France; JC136.

NCBI tax ID(s): 1465754 (species)

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General

@ref: 20277

BacDive-ID: 24536

DSM-Number: 25383

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative

description: Alistipes timonensis JC136 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human fecal flora of a healthy patient.

NCBI tax id

  • NCBI tax id: 1465754
  • Matching level: species

strain history

@refhistory
20277<- J.-C. Lagier, Timone Hospital, Marseille, France; JC136
67770DSM 25383 <-- J.-C. Lagier; Timone Hosp., France; JC136.

doi: 10.13145/bacdive24536.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Rikenellaceae
  • genus: Alistipes
  • species: Alistipes timonensis
  • full scientific name: Alistipes timonensis Lagier et al. 2014

@ref: 20277

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Rikenellaceae

genus: Alistipes

species: Alistipes timonensis

full scientific name: Alistipes timonensis Lagier et al. 2014

strain designation: JC136

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.979

colony morphology

  • @ref: 20277
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20277PYG 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
20277COLUMBIA 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

@refgrowthtypetemperaturerange
20277positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
20277anaerobe
69480anaerobe99.558

spore formation

@refspore formationconfidence
69481no100
69480no99.994

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838017632nitrate-reduction

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
68380alpha-fucosidase-3.2.1.51
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
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
20277--++--+-+/-+/---+------+----+----
20277---+--+--+-----+---+----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
20277human fecal flora of a healthy patientSenegalSENAfrica
67770Fecal flora of a healthy patient in Senegal

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7217.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_110;96_474;97_542;98_5299;99_7217&stattab=map
  • Last taxonomy: Alistipes timonensis
  • 16S sequence: JF824799
  • Sequence Identity:
  • Total samples: 14319
  • soil counts: 68
  • aquatic counts: 72
  • animal counts: 14087
  • plant counts: 92

Safety information

risk assessment

  • @ref: 20277
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20277
  • description: Alistipes timonensis JC136 16S ribosomal RNA gene, partial sequence
  • accession: JF824799
  • length: 1423
  • database: ena
  • NCBI tax ID: 1033731

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Alistipes timonensis JC136 strain DSM 253831033731.11wgspatric1033731
66792Alistipes timonensis JC1362547132133draftimg1033731
66792Alistipes timonensis DSM 253832693429854draftimg1033731
67770Alistipes timonensis JC136 P148GCA_000285455contigncbi1033731
67770Alistipes timonensis JC136 DSM 25383GCA_900107675scaffoldncbi1033731

GC content

@refGC-contentmethod
2027758.82sequence analysis
6777058.8genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.69no
flagellatedno96.64no
gram-positiveno98.603no
anaerobicyes96.943yes
aerobicno94.685yes
halophileno87.606no
spore-formingno95.673no
thermophileno96.783yes
glucose-utilyes84.498no
glucose-fermentyes57.732no

External links

@ref: 20277

culture collection no.: DSM 25383, CSUR P148, JCM 32780

straininfo link

  • @ref: 88391
  • straininfo: 402297

literature

  • topic: Genetics
  • Pubmed-ID: 23408657
  • title: Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov.
  • authors: Lagier JC, Armougom F, Mishra AK, Nguyen TT, Raoult D, Fournier PE
  • journal: Stand Genomic Sci
  • DOI: 10.4056/sigs.2685971
  • year: 2012
  • 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
20277Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25383Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25383)
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
88391Reimer, 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-ID402297.1