Strain identifier
BacDive ID: 165415
Type strain: 
Species: Ruminococcus torques
Strain history: Y. Benno <-- T. Mitsuoka <-- ATCC 27756 <-- L. V. Holdeman VPI B2-51.
NCBI tax ID(s): 411460 (strain), 33039 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 165415
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Ruminococcus torques JCM 6553 is an anaerobe, mesophilic bacterium that was isolated from Human feces.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 411460 | strain |
| 33039 | species |
strain history
- @ref: 67770
- history: Y. Benno <-- T. Mitsuoka <-- ATCC 27756 <-- L. V. Holdeman VPI B2-51.
doi: 10.13145/bacdive165415.20250331.9.3
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 torques
- full scientific name: Ruminococcus torques Holdeman and Moore 1974 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Mediterraneibacter torques
@ref: 67770
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Oscillospiraceae
genus: Ruminococcus
species: Ruminococcus torques
full scientific name: Ruminococcus torques Holdeman and Moore 1974
type strain: yes
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 125438 | anaerobe | 94.139 |
| 125439 | anaerobe | 99.8 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Human feces
taxonmaps
- @ref: 69479
- File name: preview.99_4600.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_2294;97_2784;98_3455;99_4600&stattab=map
- Last taxonomy: [Ruminococcus] torques subclade
- 16S sequence: L76604
- Sequence Identity:
- Total samples: 50303
- soil counts: 124
- aquatic counts: 936
- animal counts: 49154
- plant counts: 89
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | [Ruminococcus] torques gene for 16S ribosomal RNA, partial sequence | AB910746 | 1492 | nuccore | 33039 |
| 67770 | Ruminococcus torques small subunit ribosomal RNA (16S rDNA) gene | L76604 | 1418 | nuccore | 411460 |
| 124043 | Ruminococcus torques gene for 16S ribosomal RNA, partial sequence, isolate: GIFU 12126. | D14137 | 1385 | nuccore | 411460 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Ruminococcus torques ATCC 27756 | 411460.6 | wgs | patric | 411460 |
| 66792 | Blautia torques ATCC 27756 | 640963025 | draft | img | 411460 |
| 66792 | [Ruminococcus] torques ATCC 27756 | GCA_000153925 | scaffold | ncbi | 411460 |
GC content
- @ref: 67770
- GC-content: 42
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 81.804 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 94.139 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 61.648 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 98.048 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.374 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 84.012 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 66.7 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 75.9 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 79.9 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 99.8 |
External links
@ref: 67770
culture collection no.: JCM 6553, ATCC 27756, VPI B2-51
straininfo link
- @ref: 114463
- straininfo: 39159
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 26637816 | Sellimonas intestinalis gen. nov., sp. nov., isolated from human faeces. | Seo B, Yoo JE, Lee YM, Ko G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000817 | 2015 | ||
| Phylogeny | 29855844 | Description of Mediterraneibacter massiliensis, gen. nov., sp. nov., a new genus isolated from the gut microbiota of an obese patient and reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus and Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., Mediterraneibacter lactaris comb. nov., Mediterraneibacter torques comb. nov., Mediterraneibacter gnavus comb. nov. and Mediterraneibacter glycyrrhizinilyticus comb. nov. | Togo AH, Diop A, Bittar F, Maraninchi M, Valero R, Armstrong N, Dubourg G, Labas N, Richez M, Delerce J, Levasseur A, Fournier PE, Raoult D, Million M | Antonie Van Leeuwenhoek | 10.1007/s10482-018-1104-y | 2018 | Clostridium/classification/genetics, Gastrointestinal Microbiome/*genetics, Humans, Obesity/microbiology, Phenotype, Phylogeny, Ruminococcus/*classification/*genetics, Sequence Analysis, DNA | Pathogenicity |
| Phylogeny | 33986975 | Mediterraneibacter catenae SW178 sp. nov., an intestinal bacterium of feral chicken. | Wongkuna S, Ghimire S, Chankhamhaengdecha S, Janvilisri T, Scaria J | PeerJ | 10.7717/peerj.11050 | 2021 |
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |
| 114463 | Reimer, 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 identifiers | 10.60712/SI-ID39159.1 |
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |