Details of Microbe Species (MIC)

General Information of MIC (ID: MIC01137)
MIC Name Ruminococcus gnavus (firmicutes)
Body Site Gut
Lineage Kingdom: Bacteria
Phylum: Firmicutes
Class: Clostridia
Order: Clostridiales
Family: Lachnospiraceae
Genus: Mediterraneibacter
Species: Ruminococcus gnavus
Oxygen Sensitivity Obligate anaerobe
Microbial Metabolism Saccharolytic; Fermentative
Gram Positive
Host Relationship Commensal
Genome Size (bp) 3501911
Description Ruminococcus gnavus is an obligately anaerobic, Gram positive bacterium belonged to the genus Ruminococcus in the family Ruminococcaceae. It is a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide.
External Links Taxonomy ID
33038
Genome Assembly ID
ASM16947v1
GOLD Organism ID
Go0005275
Disease Relevance
          Crohn disease  [ICD-11: DD70]
             Description An inflammatory polysaccharide produced by the gut bacterium Ruminococcus gnavus bloomed during flares of symptoms in patients with Crohns disease. [1]
          Inflammatory bowel disease  [ICD-11: DD72]
             Description Ruminococcus gnavus may be an important member of the altered gut community in inflammatory bowel disease. [2]
          Septic arthritis  [ICD-11: FA10]
             Description Ruminococcus gnavus can cause septic arthritis. [3]
          Ulcerative colitis  [ICD-11: DD71]
             Description Ruminococcus gnavus was downregulated in expression of ulcerative colitis disease. [4]
Host Genetic Factors (HGFs)
          SMARCAD1
             HGF ID HGF2342 HGF Info       Class Copy Number Variation: Gene Deletion (CNV-GDe)
             Description The deletion of SMARCAD1 was significantly associated with a decrease of Ruminococcaceae gnavus (p-value<0.05). [5]
          SLC15A1
             HGF ID HGF2354 HGF Info       Class Copy Number Variation: Gene Deletion (CNV-GDe)
             Description The deletion of PepT1 could increase the abundance of Ruminococcus gnavus. [6]
          rs4476604
             HGF ID HGF2057 HGF Info       Class Single Nucleotide Polymorphism (SNP)
             Description The rs4476604 SNP was significantly associated with the abundance of Ruminococcus gnavus (p-value=0.00386). [7]
          rs2816958
             HGF ID HGF2538 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs2816958 SNP is associated with the abundance of Ruminococcus gnavus. [8]
          rs1250546
             HGF ID HGF2565 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs1250546 SNP is associated with the abundance of Ruminococcus gnavus. [8]
          rs13204742
             HGF ID HGF2560 HGF Info       Class Single Nucleotide Polymorphism (SNP)
             Description The rs13204742 SNP is associated with the abundance of Ruminococcus gnavus. [8]
          rs13126505
             HGF ID HGF2650 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs13126505 SNP is associated with the abundance of Ruminococcus gnavus. [8]
          rs3851228
             HGF ID HGF2553 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs3851228 SNP is associated with the abundance of Ruminococcus gnavus. [8]
          rs1456896
             HGF ID HGF2651 HGF Info       Class Single Nucleotide Polymorphism (SNP)
             Description The rs1456896 SNP is associated with the abundance of Ruminococcus gnavus. [8]
          rs925255
             HGF ID HGF2557 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs925255 SNP is associated with the abundance of Ruminococcus gnavus. [8]
          rs3764147
             HGF ID HGF2633 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-MV)
             Description The rs3764147 SNP is associated with the abundance of Ruminococcus gnavus. [8]
          rs6667605
             HGF ID HGF2621 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs6667605 SNP is associated with the abundance of Ruminococcus gnavus. [8]
          rs2488389
             HGF ID HGF2574 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs2488389 SNP is associated with the abundance of Ruminococcus gnavus. [8]
Host Immune Factors (HIFs)
          B cells
             HIF ID HIFC0001 HIF Info       Class B cells (BCs)
             Description Ruminococcus gnavus expressed protein "superantigens", which stimulated B cells expressing human VH3. [9]
          Interferon-6
             HIF ID HIFM0151 HIF Info       Class Cytokine (Cyt)
             Description Ruminococcus gnavus is associated with IL-6 expression. [10]
          Immunoglobulin G
             HIF ID HIFM0270 HIF Info       Class Immunoglobulin (Ig)
             Description The abundance of Ruminococcus gnavus is associated with IgG response. [10]
Environmental Factor(s)
             Disbiome ID
      20
References
1 Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide. Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):12672-12677. doi: 10.1073/pnas.1904099116. Epub 2019 Jun 10.
2 A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med. 2017 Nov 28;9(1):103. doi: 10.1186/s13073-017-0490-5.
3 Ruminococcus gnavus: an unusual pathogen in septic arthritis. Anaerobe. 2014 Dec;30:159-60. doi: 10.1016/j.anaerobe.2014.10.001. Epub 2014 Oct 13.
4 Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis. World J Gastroenterol. 2017 Jul 7;23(25):4548-4558. doi: 10.3748/wjg.v23.i25.4548.
5 Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium.Genome Biol. 2020 Mar 11;21(1):64. doi: 10.1186/s13059-020-01976-7.
6 Impact of PepT1 deletion on microbiota composition and colitis requires multiple generations.NPJ Biofilms Microbiomes. 2020 Jul 21;6(1):27. doi: 10.1038/s41522-020-0137-y.
7 FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects.Gut Microbes. 2018 Jul 4;9(4):357-368. doi: 10.1080/19490976.2018.1445956. Epub 2018 Apr 27.
8 A Microbe Associated with Sleep Revealed by a Novel Systems Genetic Analysis of the Microbiome in Collaborative Cross Mice. Genetics. 2020 Mar;214(3):719-733. doi: 10.1534/genetics.119.303013. Epub 2020 Jan 2.
9 B cell superantigens in the human intestinal microbiota.Sci Transl Med. 2019 Aug 28;11(507):eaau9356. doi: 10.1126/scitranslmed.aau9356.
10 Lupus nephritis is linked to disease-activity associated expansions and immunity to a gut commensal. Ann Rheum Dis. 2019 Jul;78(7):947-956. doi: 10.1136/annrheumdis-2018-214856. Epub 2019 Feb 19.

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