General Information of Metabolite (ID: MT110)
  Meta Name
Lipopolysaccharide
  Unify Name
Lipopolysaccharide
  Molecule Type
Microbial components
  Description    Click to Show/Hide the Detailed Description of This Metabolite
Lipopolysaccharide, one of the metabolites produced by Bacteroides, could be associated with the downregulation of the DNMT3B gene.

The epigenetic modification information of this metabolite
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation DNMT1 EM Info Oral epithelial cells . Periodontitis [1], [2]
DNA Methylation DNMT1 EM Info HaCaT cells . . [3]
DNA Methylation DNMT3A EM Info HaCaT cells . . [4], [5]
DNA Methylation DNMT3A EM Info . . . [1], [2]
DNA Methylation DNMT3B EM Info . . . [6], [7]
Histone Acetylation H3 EM Info . . . [8], [9]
Histone Acetylation H3 EM Info Oral epithelial cells lysine 9 Periodontitis [1], [2]
Histone Acetylation H4 EM Info . IL-6 . [8], [10]
Histone Acetylation H4 EM Info . . . [4], [5]
Histone Deacetylation HDAC1 EM Info hPDLSCs . Periodontitis [11]
Histone Deacetylation HDAC2 EM Info hPDLSCs . Periodontitis [11]
Histone Deacetylation HDAC6 EM Info . . . [6], [7]
Histone Deacetylation HDAC7 EM Info . . . [4], [5]
Histone Acetylation Histone EM Info TGF-beta1 cells lysine 9 . [4], [5]
Histone Phosphorylation Histone EM Info TGF-beta1 cells serine 10 . [4], [5]
Histone Acetylation Histone acetyltransferase p300 EM Info Oral epithelial cells . Periodontitis [12], [13]
Histone Demethylation JMJD3 EM Info HaCaT cells . . [4], [5]
miRNA let-7a EM Info HeLa cells . . [10]
miRNA let-7a EM Info RAW 264.7 cells . . [10]
miRNA let-7c EM Info HeLa cells . . [10]
miRNA let-7c EM Info RAW 264.7 cells . . [10]
miRNA let-7d EM Info HeLa cells . . [10]
miRNA let-7d EM Info RAW 264.7 cells . . [10]
miRNA let-7f EM Info HeLa cells . . [10]
miRNA let-7f EM Info RAW 264.7 cells . . [10]
miRNA let-7f EM Info THP-1 cells . Cigarette smoke [11]
miRNA let-7f EM Info THP-1 cells SOCS4 Cigarette smoke [3]
miRNA let-7f EM Info THP-1 cells TSP-1 Cigarette smoke [3]
miRNA let-7i EM Info HeLa cells . . [10]
miRNA let-7i EM Info RAW 264.7 cells . . [10]
miRNA miR-1308 EM Info HeLa cells . . [10]
miRNA miR-146a EM Info RAW 264.7 cells . . [10]
miRNA miR-146a EM Info THP-1 cells . Cigarette smoke [3]
miRNA miR-146b EM Info RAW 264.7 cells . . [10]
miRNA miR-155 EM Info RAW 264.7 cells . . [10]
miRNA miR-21 EM Info RAW 264.7 cells . . [10]
miRNA miR-29b EM Info THP-1 cells . Cigarette smoke [11]
miRNA miR-29b EM Info THP-1 cells IFI30 Cigarette smoke [3]
miRNA miR-29b EM Info THP-1 cells IL-6R-alpha Cigarette smoke [3]
miRNA miR-32 EM Info THP-1 cells . Cigarette smoke [3]
miRNA miR-891a EM Info THP-1 cells . Cigarette smoke [3]
miRNA miR-98 EM Info RAW 264.7 cells . . [10]

The microbes that produce this metabolite
      Fusobacterium nucleatum
         Detailed Information MIC Info click to show the detail information of this Microbiota [14], [11]
         Description
Fusobacteria nucleatum is a species of gram-negative, anaerobic bacteria from the genus Fusobacteria.
      Bacteroides
         Detailed Information MIC Info click to show the detail information of this Microbiota [15]
         Description
Bacteroides is a genus of gram-negative, obligate anaerobic bacteria.
      Escherichia coli
         Detailed Information MIC Info click to show the detail information of this Microbiota [16], [17]
         Description
Escherichia coli, also known as E. coli, is a gram-negative, facultative anaerobic, rod-shaped, coliform bacteria of the genus Escherichia.
      Bacteroidetes
         Detailed Information MIC Info click to show the detail information of this Microbiota [15], [18]
         Description
The phylum "Bacteroidetes" is composed of three large classes of gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals.
      Bacteroides dorei
         Detailed Information MIC Info click to show the detail information of this Microbiota [4], [19]
         Description
Bacteroides dorei are gram-negative bacteria that are anaerobic rods.
      Bacteroides ovatus
         Detailed Information MIC Info click to show the detail information of this Microbiota [1], [2]
         Description
Bacteroides ovatus is an obligate anaerobic, gram-negative common human gut bacteria. It is part of the normal human gut flora, however it is the least common of the Bacteroides intestinal isolates. It has also been associated with Coeliac disease.
      Bacteroides uniformis
         Detailed Information MIC Info click to show the detail information of this Microbiota [4], [19]
         Description
Bacteroides uniformis is a species of anaerobic, gram-negative, rod shaped bacteria assigned to the phylum Bacteroidetes. It is found in the human and swine intestinal tract, but can be pathogenic in other locations.
      Bacteroides vulgatus
         Detailed Information MIC Info click to show the detail information of this Microbiota [4], [19]
         Description
Bacteroides vulgatus is an anaerobic, gram-negative among the most commonly isolated microbes from the human gastrointestinal tract, and it has been found to constitute part of the core gut microbiota in healthy humans. It is generally considered to be a beneficial gut commensal, but studies also suggest that important intraspecies variations may exist, with specific strains of B. vulgatus shown to be capable of promoting or protecting against colitis.
      Bacteroidales
         Detailed Information MIC Info click to show the detail information of this Microbiota [8], [4]
         Description
Bacteroidales is an order of bacteria. Notably it includes the genera Prevotella and Bacteroides, which are commonly found in the human gut microbiota.
      Prevotella spp.
         Detailed Information MIC Info click to show the detail information of this Microbiota [4], [19]
         Description
Prevotella is a genus of gram-negative bacteria. Prevotella spp. are members of the oral, vaginal, and gut microbiota and are often recovered from anaerobic infections of the respiratory tract. These infections include aspiration pneumonia, lung abscess, pulmonary empyema, and chronic otitis media and sinusitis.
      Bacteroides caccae
         Detailed Information MIC Info click to show the detail information of this Microbiota [4], [19]
         Description
Bacteroides caccae is a saccharolytic gram-negative bacteria from the genus Bacteroides. They are obligate anaerobics first isolated from human feces in the 1980s.
      Bacteroides fragilis
         Detailed Information MIC Info click to show the detail information of this Microbiota [4], [19]
         Description
Bacteroides fragilis is an obligately anaerobic, gram-negative, rod-shaped bacteria. It is part of the normal microbiota of the human colon and is generally commensal, but can cause infection if displaced into the bloodstream or surrounding tissue following surgery, disease or trauma.
      Bacteroides stercoris
         Detailed Information MIC Info click to show the detail information of this Microbiota [4], [19]
         Description
Bacteroides stercoris is a species of gram-negative, obligate anaerobic bacteria.
      Bacteroides thetaiotaomicron
         Detailed Information MIC Info click to show the detail information of this Microbiota [8], [9]
         Description
Bacteroides thetaiotaomicron is a species of bacteria of the genus Bacteroides. It is a gram-negative obligate anaerobic. It is one of the most common bacteria found in human gut microbiota and is also an opportunistic pathogen.
      Salmonella
         Detailed Information MIC Info click to show the detail information of this Microbiota [8], [5]
         Description
Salmonella is a genus of rod-shaped gram-negative bacteria of the family Enterobacteriaceae.
      Prevotella copri
         Detailed Information MIC Info click to show the detail information of this Microbiota [4], [19]
         Description
Prevotella copri is a gram-negative bacteria. The cells are anaerobic and do not form spores. Prevotella copri is an intestinal bacteria, and its anaerobic qualities allows it to grow successfully in the human gut and intestines. This bacteria was found associated with Inflammatory bowel disease.
      Aggregatibacter actinomycetemcomitans
         Detailed Information MIC Info click to show the detail information of this Microbiota [3]
         Description
#N/A
      Porphyromonas gingivalis
         Detailed Information MIC Info click to show the detail information of this Microbiota [11]
         Description
Porphyromonas gingivalis belongs to the phylum Bacteroidetes and is a nonmotile, gram-negative, rod-shaped, anaerobic, pathogenic bacteria. It forms black colonies on blood agar.
      Alistipes spp.
         Detailed Information MIC Info click to show the detail information of this Microbiota [4], [19]
         Description
Lactobacillus is a genus of gram-positive, facultative anaerobic or microaerophilic, rod-shaped, non-spore-forming bacteria. They are a major part of the lactic acid bacteria group. In humans, they constitute a significant component of the microbiota at a number of body sites, such as the digestive system, urinary system, and genital system.

References
1 Daidzein Intake Is Associated with Equol Producing Status through an Increase in the Intestinal Bacteria Responsible for Equol Production. Nutrients. 2019 Feb 19;11(2):433. doi: 10.3390/nu11020433.
2 Histone lysine trimethylation or acetylation can be modulated by phytoestrogen, estrogen or anti-HDAC in breast cancer cell lines. Epigenomics. 2013 Feb;5(1):51-63. doi: 10.2217/epi.12.74.
3 MicroRNAs responsive to Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis LPS modulate expression of genes regulating innate immunity in human macrophages. Innate Immun. 2014 Jul;20(5):540-51. doi: 10.1177/1753425913501914. Epub 2013 Sep 23.
4 Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling mSystems. 2017 Nov 14;2(6):e00046-17. doi: 10.1128/mSystems.00046-17. eCollection 2017 Nov-Dec.
5 Transforming growth factor-beta 1 inhibits non-pathogenic Gram negative bacteria-induced NF-kappa B recruitment to the interleukin-6 gene promoter in intestinal epithelial cells through modulation of histone acetylation J Biol Chem. 2003 Jun 27;278(26):23851-60. doi: 10.1074/jbc.M300075200. Epub 2003 Apr 2.
6 Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells. 2010 Apr;28(4):713-20. doi: 10.1002/stem.402.
7 Dietary proline supplementation alters colonic luminal microbiota and bacterial metabolite composition between days 45 and 70 of pregnancy in Huanjiang mini-pigs J Anim Sci Biotechnol. 2018 Jan 30;9:18. doi: 10.1186/s40104-018-0233-5. eCollection 2018.
8 Dietary metabolites derived from gut microbiota: critical modulators of epigenetic changes in mammals. Nutr Rev. 2017 May 1;75(5):374-389. doi: 10.1093/nutrit/nux001.
9 Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans Cell. 2016 May 5;165(4):842-53. doi: 10.1016/j.cell.2016.04.007. Epub 2016 Apr 28.
10 Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family EMBO J. 2011 May 18;30(10):1977-89. doi: 10.1038/emboj.2011.94. Epub 2011 Apr 5.
11 Short-chain fatty acids from periodontal pathogens suppress histone deacetylases, EZH2, and SUV39H1 to promote Kaposi's sarcoma-associated herpesvirus replication. J Virol. 2014 Apr;88(8):4466-79. doi: 10.1128/JVI.03326-13. Epub 2014 Feb 5.
12 Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature. 2013 Dec 19;504(7480):446-50. doi: 10.1038/nature12721. Epub 2013 Nov 13.
13 Reactivation of latent HIV-1 by a wide variety of butyric acid-producing bacteria Cell Mol Life Sci. 2012 Aug;69(15):2583-92. doi: 10.1007/s00018-012-0936-2. Epub 2012 Feb 10.
14 Crosstalk between the microbiome and epigenome: messages from bugs. J Biochem. 2018 Feb 1;163(2):105-112. doi: 10.1093/jb/mvx080.
15 Gut Microbiota as Important Mediator Between Diet and DNA Methylation and Histone Modifications in the Host. Nutrients. 2020 Feb 25;12(3):597. doi: 10.3390/nu12030597.
16 S-Adenosylmethionine Treatment of Colorectal Cancer Cell Lines Alters DNA Methylation, DNA Repair and Tumor Progression-Related Gene Expression. Cells. 2020 Aug 9;9(8):1864. doi: 10.3390/cells9081864.
17 Progress in the microbial production of S-adenosyl-L-methionine World J Microbiol Biotechnol. 2016 Sep;32(9):153. doi: 10.1007/s11274-016-2102-8. Epub 2016 Jul 27.
18 Holocarboxylase synthetase regulates expression of biotin transporters by chromatin remodeling events at the SMVT locus. J Nutr Biochem. 2008 Jun;19(6):400-8. doi: 10.1016/j.jnutbio.2007.06.002. Epub 2007 Sep 27.
19 Epigenetic Modifications of Histones in Periodontal Disease. J Dent Res. 2016 Feb;95(2):215-22. doi: 10.1177/0022034515611876. Epub 2015 Oct 23.

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