Strain identifier

BacDive ID: 17685

Type strain: Yes

Species: Ruminococcus gauvreauii

Strain Designation: CCRI-16110

Strain history: CCUG 54292 <-- M.-C. Domingo and M. G. Bergeron CCRI-16110.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8338

BacDive-ID: 17685

DSM-Number: 19829

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, coccus-shaped

description: Ruminococcus gauvreauii CCRI-16110 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from human faecal specimen.

NCBI tax id

NCBI tax idMatching level
438033species
1123075strain

strain history

@refhistory
8338<- M.-C. Domingo; CCRI-16110
67770CCUG 54292 <-- M.-C. Domingo and M. G. Bergeron CCRI-16110.

doi: 10.13145/bacdive17685.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Oscillospiraceae
  • genus: Ruminococcus
  • species: Ruminococcus gauvreauii
  • full scientific name: Ruminococcus gauvreauii Domingo et al. 2008

@ref: 8338

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Ruminococcus

species: Ruminococcus gauvreauii

full scientific name: Ruminococcus gauvreauii Domingo et al. 2008

strain designation: CCRI-16110

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
32285positive0.75 µmcoccus-shapedno
69480positive100

colony morphology

  • @ref: 60126
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 8338
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: 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
8338positivegrowth37mesophilic
32285positivegrowth35-37mesophilic
60126positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8338anaerobe
32285anaerobe
60126anaerobe
69480anaerobe99.999

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 91.691

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-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
32285acid phosphatase+3.1.3.2
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
8338-----------------------------
8338-----------+-----------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
8338human faecal specimenQuebecCanadaCANNorth America
60126Human feces (rectal swab)Québec,MontréalCanadaCANNorth America2005-12-14
67770Human feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_46467.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_21188;97_26420;98_33593;99_46467&stattab=map
  • Last taxonomy: Ruminococcus gauvreauii subclade
  • 16S sequence: LC269264
  • Sequence Identity:
  • Total samples: 1290
  • soil counts: 12
  • aquatic counts: 14
  • animal counts: 1261
  • plant counts: 3

Safety information

risk assessment

  • @ref: 8338
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8338Ruminococcus gauvreauii strain CCRI-16110 16S ribosomal RNA gene, partial sequenceEF5296201456ena438033
67770Ruminococcus gauvreauii gene for 16S ribosomal RNA, partial sequence, strain: JCM 14987LC2692641473ena438033

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ruminococcus gauvreauii DSM 198291123075.3wgspatric1123075
66792Ruminococcus gauvreauii DSM 198292524023243draftimg1123075
67770Ruminococcus gauvreauii DSM 19829GCA_000425525scaffoldncbi1123075
66792Ruminococcus gauvreauii DSM 19829GCA_025151995completencbi438033
66792Ruminococcus gauvreauii strain DSM 19829438033.9completepatric438033

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes57no
motileno88.465no
flagellatedno91.293yes
gram-positiveyes90.765yes
anaerobicyes98.725yes
aerobicno98.003yes
halophileno89.547no
spore-formingyes55.64no
glucose-fermentyes56.278no
thermophileno99.058yes
glucose-utilyes89.362no

External links

@ref: 8338

culture collection no.: DSM 19829, CCUG 54292, JCM 14987, NML 060141, CIP 109512

straininfo link

  • @ref: 86676
  • straininfo: 401429

literature

  • topic: Phylogeny
  • Pubmed-ID: 18523184
  • title: Ruminococcus gauvreauii sp. nov., a glycopeptide-resistant species isolated from a human faecal specimen.
  • authors: Domingo MC, Huletsky A, Boissinot M, Bernard KA, Picard FJ, Bergeron MG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65259-0
  • year: 2008
  • mesh: Anaerobiosis, Anti-Bacterial Agents/pharmacology, Bacterial Proteins/genetics, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Feces/*microbiology, Genes, rRNA, Glycopeptides/pharmacology, Humans, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Ruminococcus/*classification/*drug effects/isolation & purification/physiology, Sequence Analysis, DNA, Species Specificity, *Vancomycin Resistance
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8338Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19829)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19829
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
32285Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2852528776041
60126Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54292)https://www.ccug.se/strain?id=54292
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
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)
86676Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401429.1StrainInfo: A central database for resolving microbial strain identifiers