Strain identifier
BacDive ID: 17685
Type strain:
Species: Ruminococcus gauvreauii
Strain Designation: CCRI-16110
Strain history: CCUG 54292 <-- M.-C. Domingo and M. G. Bergeron CCRI-16110.
NCBI tax ID(s): 1123075 (strain), 438033 (species)
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 id | Matching level |
---|---|
438033 | species |
1123075 | strain |
strain history
@ref | history |
---|---|
8338 | <- M.-C. Domingo; CCRI-16110 |
67770 | CCUG 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
@ref | gram stain | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|
32285 | positive | 0.75 µm | coccus-shaped | no | |
69480 | positive | 100 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
8338 | positive | growth | 37 | mesophilic |
32285 | positive | growth | 35-37 | mesophilic |
60126 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
8338 | anaerobe | |
32285 | anaerobe | |
60126 | anaerobe | |
69480 | anaerobe | 99.999 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 91.691
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | 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
@ref | value | activity | ec |
---|---|---|---|
32285 | acid phosphatase | + | 3.1.3.2 |
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | - | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | - | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8338 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
8338 | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
8338 | human faecal specimen | Quebec | Canada | CAN | North America | |
60126 | Human feces (rectal swab) | Québec,Montréal | Canada | CAN | North America | 2005-12-14 |
67770 | Human feces |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
8338 | Ruminococcus gauvreauii strain CCRI-16110 16S ribosomal RNA gene, partial sequence | EF529620 | 1456 | ena | 438033 |
67770 | Ruminococcus gauvreauii gene for 16S ribosomal RNA, partial sequence, strain: JCM 14987 | LC269264 | 1473 | ena | 438033 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Ruminococcus gauvreauii DSM 19829 | 1123075.3 | wgs | patric | 1123075 |
66792 | Ruminococcus gauvreauii DSM 19829 | 2524023243 | draft | img | 1123075 |
67770 | Ruminococcus gauvreauii DSM 19829 | GCA_000425525 | scaffold | ncbi | 1123075 |
66792 | Ruminococcus gauvreauii DSM 19829 | GCA_025151995 | complete | ncbi | 438033 |
66792 | Ruminococcus gauvreauii strain DSM 19829 | 438033.9 | complete | patric | 438033 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 57 | no |
motile | no | 88.465 | no |
flagellated | no | 91.293 | yes |
gram-positive | yes | 90.765 | yes |
anaerobic | yes | 98.725 | yes |
aerobic | no | 98.003 | yes |
halophile | no | 89.547 | no |
spore-forming | yes | 55.64 | no |
glucose-ferment | yes | 56.278 | no |
thermophile | no | 99.058 | yes |
glucose-util | yes | 89.362 | no |
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
8338 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19829) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19829 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
32285 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28525 | 28776041 | |
60126 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 54292) | https://www.ccug.se/strain?id=54292 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68380 | Automatically annotated from API rID32A | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
86676 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401429.1 | StrainInfo: A central database for resolving microbial strain identifiers |