Details of Microbe Species (MIC)

General Information of MIC (ID: MC0083)
  MIC Name
Escherichia coli
  Synonym
Bacillus coli
  Lineage Kingdom: Bacteria
Phylum: Proteobacteria
Class: Gammaproteobacteria
Order: Enterobacterales
Family: Enterobacteriaceae
Genus: Escherichia
  Oxygen Sensitivity
Facultative anaerobe
  Microbial Metabolism
Saccharolytic; Respiratory or Fermentative
  Gram
Negative
  Host Relationship
Commensal
  Genome Size (bp)
5140092
  No. of Coding Genes
5494
  No. of Non-Coding Genes
113
  No. of Small Non-Coding Genes
113
  No. of Gene Transcripts
5607
  No. of Base Pairs
5443340
  Description
Escherichia coli, also known as E. coli, is a gram-negative, facultative anaerobic, rod-shaped, coliform bacteria of the genus Escherichia.
  External Links Taxonomy ID 562
GutMDisorder ID gm0305
Genome Assembly ID ASM301845v1
GOLD Database ID Go0001810
GIMICA ID MIC00516

Full List of Metabolite(s) Produced by This MIC
     Molecule Type: Fatty acids
           Metabolite Name: Acetate Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [end-products]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
Histone Acetylation H3K27 EM Info HepG2 cells FASN promoter Hypoxia [1], [2]
Histone Acetylation H3K56 EM Info HepG2 cells FASN promoter Hypoxia [1], [2]
Histone Acetylation H3K9 EM Info HepG2 cells ACACA promoter Hypoxia [1], [2]
Histone Acetylation H4 EM Info Eosinophil cell Foxo3A promoter Asthma [1], [2]
Histone Acetylation H3K27 EM Info HepG2 cells LDHA promoter Hypoxia [2], [3]
Histone Acetylation H3K9 EM Info HepG2 cells LDHA promoter Hypoxia [2], [3]
Histone Deacetylation HDAC9 EM Info Eosinophil cell . Asthma [1], [2]
           Metabolite Name: Propionate Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [end-products]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
Histone Propionylation H3 EM Info Primary myocytes lysine 23 Health [4], [5]
Histone Propionylation H3K23 EM Info C2C12 cells Myod . [4], [5]
     Molecule Type: Microbial cell components
           Metabolite Name: Lipopolysaccharide Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial cell components
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation DNMT3A EM Info . . . [6], [7]
DNA Methylation DNMT1 EM Info Oral epithelial cells . Periodontitis [4], [5]
DNA Methylation DNMT3B EM Info . . . [8], [6]
Histone Acetylation H3 EM Info Oral epithelial cells lysine 9 Periodontitis [4], [5]
Histone Acetylation H4 EM Info . . . [4], [5]
Histone Acetylation Histone EM Info TGF-beta1 cells lysine 9 . [4], [5]
Histone Deacetylation HDAC7 EM Info . . . [4], [5]
Histone Deacetylation HDAC6 EM Info . . . [8], [6]
Histone Phosphorylation Histone EM Info TGF-beta1 cells serine 10 . [4], [5]
     Molecule Type: Other metabolites
           Metabolite Name: Inositol phosphate Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [intermediate]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
Histone Acetylation H3K9 EM Info Intestinal epithelial cells Clec2e Iintestinal disease [9], [10]
Histone Acetylation H3K9 EM Info Intestinal epithelial cells Scd2 Iintestinal disease [9], [10]
Histone Deacetylation HDAC3 EM Info Intestinal epithelial cells . Iintestinal disease [6], [11]
           Metabolite Name: Inositol trisphosphate (IP3) Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [others]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
Histone Deacetylation HDAC3 EM Info Enterocytes . Intestinal diseases [6], [11]
           Metabolite Name: S-Adenosyl Methionine (SAM) Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [intermediate]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA hypermethylation SLC39A6 EM Info HT-29 cells Cg04447424 Colorectal carcinoma [6], [12]
DNA hypermethylation ASB7 EM Info HT-29 cells Cg20072001 Colorectal carcinoma [6], [13]
DNA hypermethylation MIR636 EM Info HT-29 cells Cg21028463 Colorectal carcinoma [6], [14]
DNA Hypomethylation TSPAN11 EM Info HT-29 cells Cg20372004 Colorectal carcinoma [6], [15]
DNA Hypomethylation TAL1 EM Info SW480 cells Cg11766986 Colorectal carcinoma [6], [15]
DNA Hypomethylation CRISPLD1 EM Info HT-29 cells Cg15953602 Colorectal carcinoma [6], [12]
DNA Hypomethylation PAK7 EM Info HT-29 cells Cg22457984 Colorectal carcinoma [6], [12]
DNA Hypomethylation SNORA49 EM Info HT-29 cells Cg07588358 Colorectal carcinoma [6], [12]
DNA Hypomethylation CYP4F22 EM Info HT-29 cells Cg24456663 Colorectal carcinoma [6], [13]
DNA Hypomethylation GATA4 EM Info HT-29 cells Cg14900471 Colorectal carcinoma [6], [13]
DNA Hypomethylation TP53INP1 EM Info HT-29 cells Cg13393036 Colorectal carcinoma [16], [5]
DNA Hypomethylation HAAO EM Info SW480 cells Cg08421126 Colorectal carcinoma [4], [5]
DNA Hypomethylation TAL1 EM Info SW480 cells Cg11432900 Colorectal carcinoma [4], [5]
DNA Hypomethylation DTX1 EM Info HT-29 cells Cg22685245 Colorectal carcinoma [17], [18]
DNA Hypomethylation MYOCD EM Info HT-29 cells Cg20062401 Colorectal carcinoma [8], [6]
DNA Hypomethylation SEZ6L EM Info HT-29 cells Cg09983462 Colorectal carcinoma [8], [6]
Histone Methylation H3K4 EM Info RAW 264.7 cells TNF-Alpha promoter . [6], [15]
     Molecule Type: Phenolic compounds
           Metabolite Name: Phenolic acid Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [intermediate]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation DNMT EM Info . . . [4], [5]
     Molecule Type: Tryptophan metabolites
           Metabolite Name: Indole Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [precursors]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation DNMT EM Info . . . [19], [10]
           Metabolite Name: Indole-3-acetate Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [others]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation DNMT EM Info . . . [19], [10]
           Metabolite Name: Indole-3-aldehyde Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [others]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation DNMT EM Info . . . [9], [10]
           Metabolite Name: Indole-3-carboxaldehyde Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [others]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation DNMT EM Info . . . [9], [10]
           Metabolite Name: Indole-3-Propionate Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [others]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation DNMT EM Info . . . [9], [10]
           Metabolite Name: Kynurenine Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [intermediate]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells AGRP . [6], [11]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells ARNT2 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells ASCL1 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells AVP . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells BMP7 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells CARTPT . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells CCK . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells CORT . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells CRH . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells GALP . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells GAST . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells GHRH . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells GNRH2 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells HCRT . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells HMX2 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells KISS1 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells LHX1 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells NKX2-1 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells NPVF . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells NPW . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells NPY . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells NR5A1 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells OTP . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells OXT . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells PDYN . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells PENK . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells PNOC . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells POMC . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells POU3F2 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells PRLH . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells RAX . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells SHH . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells SIM1 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells SIX3 . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells SST . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells TRH . [6], [7]
Histone O-GlcNAcylation H2AS40 EM Info hiPSC-derived neural cells VAX1 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells AGRP . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells ARNT2 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells ASCL1 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells AVP . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells BMP7 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells CARTPT . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells CCK . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells CORT . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells CRH . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells GALP . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells GAST . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells GHRH . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells GNRH2 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells HCRT . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells HMX2 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells KISS1 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells LHX1 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells NKX2-1 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells NPVF . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells NPW . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells NPY . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells NR5A1 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells OTP . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells OXT . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells PDYN . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells PENK . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells PNOC . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells POMC . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells POU3F2 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells PRLH . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells RAX . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells SHH . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells SIM1 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells SIX3 . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells SST . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells TRH . [6], [7]
Histone Trimethylation H3K4 EM Info hiPSC-derived neural cells VAX1 . [6], [7]
           Metabolite Name: Serotonin Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [others]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation SLC6A4 EM Info T cells promoter Health [4], [5]
           Metabolite Name: Tryptamine Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [intermediate]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation DNMT EM Info . . . [6], [20]
     Molecule Type: Vitamins
           Metabolite Name: Biotin (B7) Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [others]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
Histone Biotinylation H4K12 EM Info Jurkat cells SMVT promoter 1 . [2], [21]
Histone Biotinylation H2AK9 EM Info Jurkat cells IL-2 promoter . [2], [21]
           Metabolite Name: Cobalamin (B12) Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [others]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Hypermethylation DNMT3A EM Info Hippocampal cells promoter Bacterial meningitis [6]
DNA Hypermethylation Ccl3 EM Info Hippocampal cells promoter Bacterial meningitis [6]
           Metabolite Name: Folate (B9) Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [others]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation MGMT EM Info Serum CpG site . [1], [22]
DNA Methylation Ccl3 EM Info Hippocampal cells Promoter . [6]
DNA Methylation p16 EM Info Serum CpG site . [23]
DNA Methylation MLH1 EM Info Serum CpG site . [17], [18]
miRNA miR-22-3p EM Info HL-7702 cells . Normal [6]
miRNA miR-22-3p EM Info QGY-7703 cells . Normal [6]
miRNA miR-149-5p EM Info HL-7702 cells . Normal [6]
miRNA miR-149-5p EM Info QGY-7703 cells . Normal [6], [24]
           Metabolite Name: Niacin (B3) Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [precursors]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
Histone Acetylation H3 EM Info Primary lymphocytes FXN Friedreich's ataxia [4], [5]
Histone Acetylation H4 EM Info Primary lymphocytes FXN Friedreich's ataxia [4], [5]
Histone Trimethylation H3K27 EM Info Primary lymphocytes FXN Friedreich's ataxia [4], [5]
Histone Trimethylation H3K9 EM Info Primary lymphocytes FXN Friedreich's ataxia [4], [5]
           Metabolite Name: Riboflavin (B2) Click to Show/Hide
              Detailed Infomation Meta Info click to show the detail information of this Metabolite
              Metabolic Classification Microbial producted compound [precursors]
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
DNA Methylation Zac1 EM Info . . . [25]
DNA Methylation LINE-1 EM Info Peripheral blood leukocyte CpG sites MTHFR 677TT genotype [25]
DNA Methylation GNA12 EM Info Peripheral blood leukocyte Promoter MTHFR C677T polymorphism [6], [26]
DNA Methylation IGF2 EM Info Peripheral blood leukocyte DMR2 MTHFR C677T polymorphism [6], [27]
DNA Methylation MTHFR EM Info Peripheral blood leukocyte north shore MTHFR 677TT genotype [6], [14]
DNA Methylation AGTR1 EM Info Peripheral blood leukocyte Promoter MTHFR C677T polymorphism [6], [28]
Histone Methylation H3K4 EM Info MGC-803 cells LSD1 Gastric cancer [25]

Full List of Protein(s) Produced by This MIC
     Protein Type: Microbial secreted proteins
           Protein Name: hlyA Click to Show/Hide
              Detailed Infomation Pro Info click to show the detail information of this protein
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
Histone Acetylation H3K9 EM Info Bladder epithelial cells CXCL8 promoter Uropathogenic Escherichia coli infection [29]
           Protein Name: NleC Click to Show/Hide
              Detailed Infomation Pro Info click to show the detail information of this protein
Modification Type Molecule EM Info Cell/Tissue Type Modified sites Condition REF
Histone Acetylation EP300 EM Info Caco-2 cells IL-8 EPEC and EHEC infection [30]

References
1 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.
2 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.
3 Epigenetic Modifications of Histones in Periodontal Disease. J Dent Res. 2016 Feb;95(2):215-22. doi: 10.1177/0022034515611876. Epub 2015 Oct 23.
4 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.
5 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.
6 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.
7 Kynurenine, 3-OH-kynurenine, and anthranilate are nutrient metabolites that alter H3K4 trimethylation and H2AS40 O-GlcNAcylation at hypothalamus-related loci. Sci Rep. 2019 Dec 24;9(1):19768. doi: 10.1038/s41598-019-56341-x.
8 Response of MiRNA-22-3p and MiRNA-149-5p to Folate Deficiency and the Differential Regulation of MTHFR Expression in Normal and Cancerous Human Hepatocytes. PLoS One. 2017 Jan 3;12(1):e0168049. doi: 10.1371/journal.pone.0168049. eCollection 2017.
9 Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia. Nat Commun. 2016 Jun 30;7:11960. doi: 10.1038/ncomms11960.
10 Fermentation Products of Commensal Bacteria Alter Enterocyte Lipid Metabolism Cell Host Microbe. 2020 Mar 11;27(3):358-375.e7. doi: 10.1016/j.chom.2020.01.028. Epub 2020 Feb 25.
11 Vitamin B(12) is neuroprotective in experimental pneumococcal meningitis through modulation of hippocampal DNA methylation. J Neuroinflammation. 2020 Apr 1;17(1):96. doi: 10.1186/s12974-020-01763-y.
12 Heterochromatinization induced by GAA-repeat hyperexpansion in Friedreich's ataxia can be reduced upon HDAC inhibition by vitamin B3. Hum Mol Genet. 2013 Jul 1;22(13):2662-75. doi: 10.1093/hmg/ddt115. Epub 2013 Mar 7.
13 DNA methylation of hypertension-related genes and effect of riboflavin supplementation in adults stratified by genotype for the MTHFR C677T polymorphism. Int J Cardiol. 2021 Jan 1;322:233-239. doi: 10.1016/j.ijcard.2020.09.011. Epub 2020 Sep 10.
14 Riboflavin supplementation alters global and gene-specific DNA methylation in adults with the MTHFR 677 TT genotype. Biochimie. 2020 Jun;173:17-26. doi: 10.1016/j.biochi.2020.04.007. Epub 2020 Apr 22.
15 High levels of circulating folate concentrations are associated with DNA methylation of tumor suppressor and repair genes p16, MLH1, and MGMT in elderly Chileans. Clin Epigenetics. 2017 Jul 24;9:74. doi: 10.1186/s13148-017-0374-y. eCollection 2017.
16 S-adenosylmethionine inhibits lipopolysaccharide-induced gene expression via modulation of histone methylation. Hepatology. 2008 May;47(5):1655-66. doi: 10.1002/hep.22231.
17 Propionate hampers differentiation and modifies histone propionylation and acetylation in skeletal muscle cells. Mech Ageing Dev. 2021 Jun;196:111495. doi: 10.1016/j.mad.2021.111495. Epub 2021 Apr 28.
18 Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes mSystems. 2019 Jul 16;4(4):e00185-19. doi: 10.1128/mSystems.00185-19.
19 Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites. Nat Commun. 2015 Jun 23;6:7320. doi: 10.1038/ncomms8320.
20 Peripheral SLC6A4 DNA methylation is associated with in vivo measures of human brain serotonin synthesis and childhood physical aggression. PLoS One. 2012;7(6):e39501. doi: 10.1371/journal.pone.0039501. Epub 2012 Jun 20.
21 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.
22 Biosynthesis of Vitamins by Probiotic Bacteria.
23 Microbiota-mediated phytate metabolism activates HDAC3 to contribute intestinal homeostasis. Signal Transduct Target Ther. 2020 Sep 21;5(1):211. doi: 10.1038/s41392-020-00321-5.
24 Effect of phenolic acids of microbial origin on production of reactive oxygen species in mitochondria and neutrophils J Biomed Sci. 2012 Oct 12;19(1):89. doi: 10.1186/1423-0127-19-89.
25 Microbiota-derived metabolite promotes HDAC3 activity in the gut. Nature. 2020 Oct;586(7827):108-112. doi: 10.1038/s41586-020-2604-2. Epub 2020 Jul 30.
26 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.
27 Lysine-specific demethylase 1 activation by vitamin B2 attenuates efficacy of apatinib for proliferation and migration of gastric cancer cell MGC-803. J Cell Biochem. 2018 Jun;119(6):4957-4966. doi: 10.1002/jcb.26741. Epub 2018 Mar 9.
28 Biotinylation of histones represses transposable elements in human and mouse cells and cell lines and in Drosophila melanogaster. J Nutr. 2008 Dec;138(12):2316-22. doi: 10.3945/jn.108.098673.
29 Uropathogenic Escherichia coli Virulence Factor alpha-Hemolysin Reduces Histone Acetylation to Inhibit Expression of Proinflammatory Cytokine Genes J Infect Dis. 2021 Mar 29;223(6):1040-1051. doi: 10.1093/infdis/jiab018.
30 The pathogenic Escherichia coli type III secreted protease NleC degrades the host acetyltransferase p300. Cell Microbiol. 2011 Oct;13(10):1542-57. doi: 10.1111/j.1462-5822.2011.01640.x. Epub 2011 Aug 4.

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