General Information of MIC (ID: MIC01140)
MIC Name	Ruminococcus sp. (firmicutes)
Body Site	Gut
Lineage	Kingdom: Bacteria Phylum: Firmicutes Class: Clostridia Order: Clostridiales Family: Ruminococcaceae Genus: Ruminococcus Species: Ruminococcus sp.
Oxygen Sensitivity	Obligate anaerobe
Microbial Metabolism	Saccharolytic; Fermentative; Utilize hydrogen as energy source
Gram	Structurally positive but stains negative
Host Relationship	Commensal
Description	Ruminococcus is a genus of bacteria in the class Clostridia. They are anaerobic, saccharolytic, fermentative, Gram-positive gut microbes.
External Links	Taxonomy ID	41978
	GOLD Organism ID	Go0003380
Disease Relevance
Chagas disease  [ICD-11: 1F53]
Description	Ruminococcaceae was associated with chagas disease.				[1]
Non-alcoholic fatty liver disease  [ICD-11: DB92]
Description	Ruminococcus was associated with nonalcoholic fatty liver disease.				[2]
Ulcerative colitis  [ICD-11: DD71]
Description	The differences at the phylum level between the Ulcerative colitis and Familial adenomatous polyposis cohorts corresponded to significant increases in the levels of the proteobacterial families Comamonadaceae, Moraxellaceae and Alcaligenaceae in tandem with a significant reduction in the Bacteroidetes families Bacteroidaceae and Prevotellaceae and the Firmicutes family Ruminococcaceae in Ulcerative colitis.				[3]

Host Genetic Factors (HGFs)
C4B
HGF ID	HGF2348	HGF Info	Class	Copy Number Variation: Gene Duplication (CNV-GDu)
Description	The low C4B-CN has been significantly associated with the high abundance of Ruminococcus (p-value<0.05).				[4]
15q11-13
HGF ID	HGF2318	HGF Info	Class	Copy Number Variation: Gene Duplication (CNV-GDu)
Description	There has a significantly different abundance of Ruminococcus sp. between 15q dup mice and wide type littermates (p-value=0.0453).				[5]
KLB
HGF ID	HGF2334	HGF Info	Class	Copy Number Variation: Gene Deletion (CNV-GDe)
Description	The deletion of KLB reduced the proportion of Ruminococcus.				[6]
TLR2
HGF ID	HGF2319	HGF Info	Class	Copy Number Variation: Gene Deletion (CNV-GDe)
Description	The deletion of TLR2 increased the abundance of Ruminococcus.				[7]
AMY1A
HGF ID	HGF2311	HGF Info	Class	Copy Number Variation: Gene Duplication (CNV-GDu)
Description	Gut microbiome Ruminococcus differs between high AMY1-CN and low AMY1-CN groups at the OTU Level (p-value<0.05).				[8]
TNFSF15
HGF ID	HGF2324	HGF Info	Class	Copy Number Variation: Gene Deletion (CNV-GDe)
Description	The deletion of TNFSF15 is significantly associated with the abundance of Ruminococcaceae bacterium (p-value=3.32E-05).				[9]
MUC2
HGF ID	HGF2331	HGF Info	Class	Copy Number Variation: Gene Deletion (CNV-GDe)
Description	The deletion of MUC2 showed significantly increased abundance of Ruminococcaceae (p-value<0.05).				[10]
SLC15A1
HGF ID	HGF2354	HGF Info	Class	Copy Number Variation: Gene Deletion (CNV-GDe)
Description	The deletion of PepT1 could decrease the abundance of Ruminococcaceae.				[11]
NLRP3
HGF ID	HGF2355	HGF Info	Class	Copy Number Variation: Gene Deletion (CNV-GDe)
Description	The deletion of NLRP3 could significantly increase the abundance of Ruminococcus (p-value<0.01).				[12]
hsa-miR-146a-5p
HGF ID	HGF0252	HGF Info	Class	Non-coding RNA: Micro (ncRNA-miRNA)
Description	The deletion of miR-146an increased the abundance of Ruminococcaceae.				[13]
hsa-miR-204-5p
HGF ID	HGF0207	HGF Info	Class	Non-coding RNA: Micro (ncRNA-miRNA)
Description	The vascular microRNA-204 (miR-204) expression is significantly downregulated by Ruminococcus (p-value<0.05).				[14]
rs7156837
HGF ID	HGF1302	HGF Info	Class	Single Nucleotide Polymorphism: Intron variant (SNP-IV)
Description	The rs7156837 SNP was significantly associated with the abundance of Ruminococcus (p-value=1.95E-07).				[15]
rs4889839
HGF ID	HGF1358	HGF Info	Class	Single Nucleotide Polymorphism: Intron variant (SNP-IV)
Description	The rs4889839 SNP was significantly associated with the abundance of Ruminococcus (p-value=6.06926E-07).				[9]
rs4460847
HGF ID	HGF2229	HGF Info	Class	Single Nucleotide Polymorphism (SNP)
Description	The rs4460847 SNP was significantly associated with the abundance of Ruminococcus (p-value=0.03505).				[16]
rs11845652
HGF ID	HGF1347	HGF Info	Class	Single Nucleotide Polymorphism: Intron variant (SNP-IV)
Description	The rs11845652 SNP was significantly associated with the abundance of Ruminococcus (p-value=7.79E-08).				[15]
rs7134375
HGF ID	HGF1645	HGF Info	Class	Single Nucleotide Polymorphism: Non coding transcript variant (SNP-NCTV)
Description	The rs7134375 SNP was significantly associated with the abundance of Ruminococcaceae(p-value=6.70E-05 ).				[17]
rs60719569
HGF ID	HGF1411	HGF Info	Class	Single Nucleotide Polymorphism: Intron variant (SNP-IV)
Description	The rs60719569 SNP was significantly associated with the abundance of Ruminococcaceae bacterium (p-value<1.00E-08).				[18]
rs4968435
HGF ID	HGF2171	HGF Info	Class	Single Nucleotide Polymorphism (SNP)
Description	The rs4968435 SNP was significantly associated with the abundance of Ruminococcaceae (p-value=4.02E-06).				[15]
rs206196
HGF ID	HGF2000	HGF Info	Class	Single Nucleotide Polymorphism (SNP)
Description	The rs206196 SNP was significantly associated with the abundance of Ruminococcaceae (p-value=9.10E-08).				[15]
rs1800795
HGF ID	HGF1720	HGF Info	Class	Single Nucleotide Polymorphism: Intron variant (SNP-IV)
Description	The variant gene IL-6 of innate immunity rs1800795 is significantly associated with the abundance of gut micriobiota Ruminococcaceae (p-value<0.0001).				[19]
rs1346183
HGF ID	HGF1613	HGF Info	Class	Single Nucleotide Polymorphism: Intron variant (SNP-IV)
Description	The rs1346183 SNP was significantly associated with the abundance of Ruminococcaceae (p-value=3.21E-08).				[15]
rs10128711
HGF ID	HGF1318	HGF Info	Class	Single Nucleotide Polymorphism: Intron variant (SNP-IV)
Description	The rs10128711 SNP was significantly associated with the abundance of Ruminococcaceae (p-value=9.78E-05 ).				[17]

Host Immune Factors (HIFs)
Programmed death-ligand 1
HIF ID	HIFM0189	HIF Info	Class	Checkpoint molecule (CM)
Description	The response to anti-PD-L1 therapy significantly correlated with fecal transplantations from patients abundant in Ruminococcaceae family.				[20]
Neutrophils
HIF ID	HIFC0029	HIF Info	Class	Granulocytes (Gra)
Description	Ruminococcus spp. at neutrophil recovery was negatively correlated with subsequent acute severe graft-versus-host disease.				[21]
Immunoglobulin M
HIF ID	HIFM0266	HIF Info	Class	Immunoglobulin (Ig)
Description	The abundance of Ruminococcaceae was associated with IgM response.				[22]
Immunoglobulin G
HIF ID	HIFM0270	HIF Info	Class	Immunoglobulin (Ig)
Description	The abundance of Ruminococcaceae was associated with IgM response.				[22]
Immunoglobulin A
HIF ID	HIFM0272	HIF Info	Class	Immunoglobulin (Ig)
Description	Ruminococcus was significantly enriched in the IgA (Low or no IgA binding) consortia.				[23]
Immunoglobulin E
HIF ID	HIFM0271	HIF Info	Class	Immunoglobulin (Ig)
Description	IgE immune responses was associated with Ruminococcaceae.				[24]
CD16+ Natural Killer cells
HIF ID	HIFC0094	HIF Info	Class	Natural killer cells (NKCs)
Description	The increased proportion of CD16+ NK cells was associated with the decrease of gut commensal bacteria(Ruminococcus).				[25]
Regulatory T cells
HIF ID	HIFC0030	HIF Info	Class	T cells (TCs)
Description	Ruminococcus is associated with regulatory T cells responses.				[26]
T helper type 17 cells
HIF ID	HIFC0080	HIF Info	Class	T cells (TCs)
Description	Ruminococcus is associated with T helper type 17(Th17)cells responses.				[26]
T-cell surface glycoprotein CD4
HIF ID	HIFM0050	HIF Info	Class	T-cell receptor (TCR)
Description	The stool of HIV-infected patients with high CD4 counts were enriched for traditional gastrointestinal genera Ruminococcus(false discovery rate q < 0.05, read difference 100 reads, and presence in 50%).				[27]

Environmental Factor(s)
Disbiome ID			132
gutMDisorder ID			gm0593

References
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2	Nonalcoholic fatty liver disease is associated with dysbiosis independent of body mass index and insulin resistance. Sci Rep. 2018 Jan 23;8(1):1466. doi: 10.1038/s41598-018-19753-9.
3	The bacteriology of pouchitis: a molecular phylogenetic analysis using 16S rRNA gene cloning and sequencing. Ann Surg. 2010 Jul;252(1):90-8. doi: 10.1097/SLA.0b013e3181e3dc8b.
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9	Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD.Gut. 2020 Jul 10:gutjnl-2019-319706. doi: 10.1136/gutjnl-2019-319706. Online ahead of print.
10	The Dynamic Changes of Gut Microbiota in Muc2 Deficient Mice.Int J Mol Sci. 2018 Sep 18;19(9):2809. doi: 10.3390/ijms19092809.
11	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.
12	Gut microbiota from NLRP3-deficient mice ameliorates depressive-like behaviors by regulating astrocyte dysfunction via circHIPK2.Microbiome. 2019 Aug 22;7(1):116. doi: 10.1186/s40168-019-0733-3.
13	AhR Activation by TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) Attenuates Pertussis Toxin-Induced Inflammatory Responses by Differential Regulation of Tregs and Th17 Cells Through Specific Targeting by microRNA. Al-Ghezi ZZ, Singh N, Mehrpouya-Bahrami P, Busbee PB, Nagarkatti M, Nagarkatti PS.. Front Microbiol. 2019 Oct 18;10:2349. doi: 10.3389/fmicb.2019.02349. eCollection 2019.
14	The importance of interaction between MicroRNAs and gut microbiota in several pathways. Behrouzi A, Ashrafian F, Mazaheri H, Lari A, Nouri M, Riazi Rad F, Hoseini Tavassol Z, Siadat SD.. Microb Pathog. 2020 Jul;144:104200. doi: 10.1016/j.micpath.2020.104200. Epub 2020 Apr 11.
15	Genetic Determinants of the Gut Microbiome in UK Twins.Cell Host Microbe. 2016 May 11;19(5):731-43. doi: 10.1016/j.chom.2016.04.017.
16	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.
17	The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids.Circ Res. 2015 Oct 9;117(9):817-24. doi: 10.1161/CIRCRESAHA.115.306807. Epub 2015 Sep 10.
18	Host genetic variation and its microbiome interactions within the Human Microbiome Project.Genome Med. 2018 Jan 29;10(1):6. doi: 10.1186/s13073-018-0515-8.
19	Variants in genes of innate immunity, appetite control and energy metabolism are associated with host cardiometabolic health and gut microbiota composition.Gut Microbes. 2020 May 3;11(3):556-568. doi: 10.1080/19490976.2019.1619440. Epub 2019 Jun 3.
20	The gut microbiome and response to immune checkpoint inhibitors: preclinical and clinical strategies.Clin Transl Med. 2019 Mar 18;8(1):9. doi: 10.1186/s40169-019-0225-x.
21	Stool Microbiota at Neutrophil Recovery Is Predictive for Severe Acute Graft vs Host Disease After Hematopoietic Cell Transplantation.Clin Infect Dis. 2017 Nov 29;65(12):1984-1991. doi: 10.1093/cid/cix699.
22	Effects of mesalazine combined with bifid triple viable on intestinal flora, immunoglobulin and levels of cal, MMP-9, and MPO in feces of patients with ulcerative colitis. Eur Rev Med Pharmacol Sci. 2020 Jan;24(2):935-942. doi: 10.26355/eurrev_202001_20079.
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24	Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow's Milk Protein Allergy under a Restricted Diet.Nutrients. 2018 Oct 11;10(10):1481. doi: 10.3390/nu10101481.
25	Dysbiosis of gut microbiome affecting small intestine morphology and immune balance: a rhesus macaque model.Zool Res. 2020 Jan 18;41(1):20-31. doi: 10.24272/j.issn.2095-8137.2020.004.
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27	Gut microbiota in HIV-pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction. Microbiome. 2019 Mar 11;7(1):37. doi: 10.1186/s40168-019-0651-4.

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