Strain identifier
BacDive ID: 165414
Type strain: 
Species: Mediterraneibacter gnavus
Strain Designation: CPI C7-9
Strain history: <- RIKEN BRC-JCM, Japan; JCM 6515
NCBI tax ID(s): 411470 (strain), 33038 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 165414
DSM-Number: 114966
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Mediterraneibacter gnavus CPI C7-9 is an anaerobe, mesophilic bacterium that was isolated from Human feces.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 33038 | species |
| 411470 | strain |
strain history
| @ref | history |
|---|---|
| 67770 | Y. Benno <-- T. Mitsuoka <-- ATCC 29149 <-- L. V. Holdeman VPI C7-9. |
| 68849 | <- RIKEN BRC-JCM, Japan; JCM 6515 |
doi: 10.13145/bacdive165414.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Mediterraneibacter
- species: Mediterraneibacter gnavus
- full scientific name: Mediterraneibacter gnavus (Moore et al. 1976) Togo et al. 2023
synonyms
- @ref: 20215
- synonym: Ruminococcus gnavus
@ref: 67770
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Lachnospiraceae
genus: Mediterraneibacter
species: Mediterraneibacter gnavus
full scientific name: Mediterraneibacter gnavus (Moore et al. 1976) Togo et al. 2023
strain designation: CPI C7-9
type strain: yes
Culture and growth conditions
culture medium
- @ref: 68849
- name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
- growth: yes
- link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium110.pdf
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 67770 | positive | growth | 37 |
| 68849 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 125438 | anaerobe | 92.956 |
| 125439 | anaerobe | 99.7 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 67770 | Human feces | ||||
| 68849 | Human feces | May be isolated within the study: Normal Flora of 20 Japanese-Hawaiians (Moore & Holdeman, Appl. Microbiol. 27:961-979 (1974) | Japan | JPN | Asia |
taxonmaps
- @ref: 69479
- File name: preview.99_2032.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_1122;97_1317;98_1590;99_2032&stattab=map
- Last taxonomy: [Ruminococcus] gnavus subclade
- 16S sequence: X94967
- Sequence Identity:
- Total samples: 18697
- soil counts: 34
- aquatic counts: 259
- animal counts: 18387
- plant counts: 17
Safety information
risk assessment
- @ref: 68849
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | [Ruminococcus] gnavus gene for 16S ribosomal RNA, partial sequence | AB910745 | 1492 | nuccore | 33038 |
| 67770 | R.gnavus 16S ribosomal RNA | X94967 | 1481 | nuccore | 411470 |
| 124043 | Ruminococcus gnavus gene for 16S ribosomal RNA, partial sequence, isolate: GIFU 12124. | D14136 | 1387 | nuccore | 411470 |
| 124043 | Ruminococcus gnavus small subunit ribosomal RNA (16S rDNA) gene. | L76597 | 1423 | nuccore | 411470 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | [Ruminococcus] gnavus ATCC 29149 | GCA_009831375 | complete | ncbi | 411470 |
| 66792 | [Ruminococcus] gnavus ATCC 29149 JCM6515 | GCA_008121495 | complete | ncbi | 411470 |
| 66792 | [Ruminococcus] gnavus | 33038.12 | wgs | patric | 33038 |
| 66792 | Ruminococcus gnavus ATCC 29149 | 411470.6 | wgs | patric | 411470 |
| 66792 | Ruminococcus gnavus ATCC 29149 | 411470.41 | wgs | patric | 411470 |
| 66792 | [Ruminococcus] gnavus ATCC 29149 | 411470.47 | complete | patric | 411470 |
| 66792 | [Ruminococcus] gnavus ATCC 29149 strain JCM6515 | 411470.46 | complete | patric | 411470 |
| 66792 | Blautia gnavus ATCC 29149 | 640963057 | draft | img | 411470 |
| 66792 | Blautia gnavus ATCC 29149 | 2811995116 | draft | img | 411470 |
| 67770 | [Ruminococcus] gnavus ATCC 29149 | GCA_000169475 | contig | ncbi | 411470 |
| 67770 | [Ruminococcus] gnavus ATCC 29149 | GCA_002959615 | contig | ncbi | 411470 |
| 66792 | [Ruminococcus] gnavus ATCC 29149 | GCA_025152275 | complete | ncbi | 411470 |
| 66792 | [Ruminococcus] gnavus ATCC 29149 | 411470.52 | complete | patric | 411470 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 67770 | 43 | thermal denaturation, midpoint method (Tm) |
| 67770 | 46.2 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 81.963 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 92.956 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 96.006 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 53.434 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.28 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 80.477 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 77.5 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 82.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 76.6 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 99.7 |
External links
@ref: 67770
culture collection no.: JCM 6515, ATCC 29149, VPI C7-9, DSM 114966
straininfo link
- @ref: 114462
- straininfo: 39379
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 24204617 | Utilisation of mucin glycans by the human gut symbiont Ruminococcus gnavus is strain-dependent. | Crost EH, Tailford LE, Le Gall G, Fons M, Henrissat B, Juge N | PLoS One | 10.1371/journal.pone.0076341 | 2013 | Base Sequence, Carbohydrate Metabolism, Gastrointestinal Tract/metabolism/*microbiology, Gene Order, Genetic Loci, Genome, Bacterial, Humans, Metabolome, Molecular Sequence Data, Mucins/*metabolism, Multigene Family, Nuclear Magnetic Resonance, Biomolecular, Polysaccharides/*metabolism, Ruminococcus/genetics/growth & development/*metabolism, *Symbiosis, Transcriptome | Genetics |
| Proteome | 24246060 | Filling out the structural map of the NTF2-like superfamily. | Eberhardt RY, Chang Y, Bateman A, Murzin AG, Axelrod HL, Hwang WC, Aravind L | BMC Bioinformatics | 10.1186/1471-2105-14-327 | 2013 | Bacterial Proteins/*chemistry, Bacteroides/chemistry, Campylobacter jejuni/chemistry, Catalytic Domain, Crystallography, X-Ray, Ligands, Nucleocytoplasmic Transport Proteins/*chemistry, Peptide Mapping/*methods, Protein Folding, Protein Multimerization, Protein Structure, Tertiary, Ruminococcus/chemistry | |
| Metabolism | 26154892 | Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation. | Tailford LE, Owen CD, Walshaw J, Crost EH, Hardy-Goddard J, Le Gall G, de Vos WM, Taylor GL, Juge N | Nat Commun | 10.1038/ncomms8624 | 2015 | Adaptation, Physiological/*physiology, Gene Expression Regulation, Bacterial/*physiology, Gene Expression Regulation, Enzymologic/physiology, Glycoproteins/genetics/*metabolism, Humans, Intestinal Mucosa/*microbiology, Mucins/metabolism, Neuraminidase/genetics/*metabolism, Ruminococcus/*enzymology/genetics/metabolism | Pathogenicity |
| Metabolism | 27223845 | The mucin-degradation strategy of Ruminococcus gnavus: The importance of intramolecular trans-sialidases. | Crost EH, Tailford LE, Monestier M, Swarbreck D, Henrissat B, Crossman LC, Juge N | Gut Microbes | 10.1080/19490976.2016.1186334 | 2016 | Bacterial Proteins/genetics/*metabolism, Genome, Bacterial, Glycoproteins/genetics/*metabolism, Mucins/*metabolism, Neuraminidase/genetics/*metabolism, Ruminococcus/enzymology/genetics/growth & development/*metabolism | Genetics |
| Phylogeny | 28556772 | Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov. | Sakamoto M, Iino T, Ohkuma M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001790 | 2017 | Bacterial Typing Techniques, Base Composition, Clostridiales/*classification/genetics/isolation & purification, Clostridium/classification, DNA, Bacterial/genetics, Eubacterium/classification, Fatty Acids/chemistry, Feces/*microbiology, Genes, Bacterial, Humans, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Pathogenicity |
| Metabolism | 29259165 | Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus. | Owen CD, Tailford LE, Monaco S, Suligoj T, Vaux L, Lallement R, Khedri Z, Yu H, Lecointe K, Walshaw J, Tribolo S, Horrex M, Bell A, Chen X, Taylor GL, Varki A, Angulo J, Juge N | Nat Commun | 10.1038/s41467-017-02109-8 | 2017 | Adhesins, Bacterial/*chemistry/genetics/metabolism, Animals, Catalytic Domain/genetics, Cell Line, Colon/cytology/metabolism, Computational Biology, Crystallography, X-Ray, Glycoproteins/*chemistry/genetics/metabolism, Goblet Cells/metabolism, Humans, Lactose/analogs & derivatives/chemistry/metabolism, Mice, Inbred C57BL, Mucins/*metabolism, Mutagenesis, Site-Directed, N-Acetylneuraminic Acid/*chemistry/metabolism, Neuraminidase/*chemistry/genetics/metabolism, Protein Binding, Ruminococcus/*enzymology, Substrate Specificity, Symbiosis | Pathogenicity |
| 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 |
| Pathogenicity | 30455672 | Mechanistic Insights Into the Cross-Feeding of Ruminococcus gnavus and Ruminococcus bromii on Host and Dietary Carbohydrates. | Crost EH, Le Gall G, Laverde-Gomez JA, Mukhopadhya I, Flint HJ, Juge N | Front Microbiol | 10.3389/fmicb.2018.02558 | 2018 | ||
| Metabolism | 32333083 | Fucosidases from the human gut symbiont Ruminococcus gnavus. | Wu H, Rebello O, Crost EH, Owen CD, Walpole S, Bennati-Granier C, Ndeh D, Monaco S, Hicks T, Colvile A, Urbanowicz PA, Walsh MA, Angulo J, Spencer DIR, Juge N | Cell Mol Life Sci | 10.1007/s00018-020-03514-x | 2020 | Bacterial Proteins/chemistry/*metabolism, Clostridiales/chemistry/enzymology/*metabolism, *Gastrointestinal Microbiome, Gastrointestinal Tract/microbiology, Glycoconjugates/metabolism, Humans, Oligosaccharides/metabolism, Polysaccharides/metabolism, Substrate Specificity, alpha-L-Fucosidase/chemistry/*metabolism | Pathogenicity |
| Metabolism | 32669363 | Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria. | Bell A, Severi E, Lee M, Monaco S, Latousakis D, Angulo J, Thomas GH, Naismith JH, Juge N | J Biol Chem | 10.1074/jbc.RA120.014454 | 2020 | Bacterial Proteins/*chemistry/genetics/metabolism, Clostridiales/*enzymology/genetics, Escherichia coli/enzymology/genetics, Genetic Complementation Test, Humans, Mucins/chemistry/metabolism, N-Acetylneuraminic Acid/*chemistry/genetics/metabolism, Oxidoreductases/*chemistry/genetics/metabolism | Enzymology |
| Phylogeny | 33512312 | Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse. | Rasmussen TS, Streidl T, Hitch TCA, Wortmann E, Deptula P, Kofoed MVW, Riedel T, Neumann-Schaal M, Hansen M, Nielsen DS, Clavel T, Vogensen FK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004673 | 2021 | ||
| Metabolism | 34936658 | The human gut symbiont Ruminococcus gnavus shows specificity to blood group A antigen during mucin glycan foraging: Implication for niche colonisation in the gastrointestinal tract. | Wu H, Crost EH, Owen CD, van Bakel W, Martinez Gascuena A, Latousakis D, Hicks T, Walpole S, Urbanowicz PA, Ndeh D, Monaco S, Sanchez Salom L, Griffiths R, Reynolds RS, Colvile A, Spencer DIR, Walsh M, Angulo J, Juge N | PLoS Biol | 10.1371/journal.pbio.3001498 | 2021 | ABO Blood-Group System/immunology, Blood Group Antigens/immunology, Clostridiales/genetics/*metabolism/physiology, Gastrointestinal Microbiome, Gastrointestinal Tract, Glycoside Hydrolases/metabolism, Humans, Mucin-1/*metabolism, Mucins/metabolism, Oligosaccharides/metabolism, Polysaccharides/metabolism, Ruminococcus/genetics/metabolism, Substrate Specificity, Tandem Mass Spectrometry/methods | Pathogenicity |
| Metabolism | 35579971 | The role of the mucin-glycan foraging Ruminococcus gnavus in the communication between the gut and the brain. | Coletto E, Latousakis D, Pontifex MG, Crost EH, Vaux L, Perez Santamarina E, Goldson A, Brion A, Hajihosseini MK, Vauzour D, Savva GM, Juge N | Gut Microbes | 10.1080/19490976.2022.2073784 | 2022 | Animals, *Brain/metabolism, *Clostridiales, *Gastrointestinal Microbiome, Mice, *Mucins/metabolism, N-Acetylneuraminic Acid/metabolism, Polysaccharides/metabolism | |
| Pathogenicity | 36032126 | Sex-dependent Lupus Blautia (Ruminococcus) gnavus strain induction of zonulin-mediated intestinal permeability and autoimmunity. | Silverman GJ, Deng J, Azzouz DF | Front Immunol | 10.3389/fimmu.2022.897971 | 2022 | Animals, Antibodies, Antinuclear, *Autoimmunity, Clostridiales, Female, *Gastrointestinal Microbiome, Haptoglobins, Humans, *Lupus Erythematosus, Systemic/microbiology, Male, Mice, Mice, Inbred C57BL, Permeability, Protein Precursors, Ruminococcus, *Sex Factors |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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/ | ||
| 68849 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-114966 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 114966) | |
| 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/ | |
| 114462 | 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-ID39379.1 | |
| 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 |