Details of Microbe Species (MIC)

General Information of MIC (ID: MC0724)
  MIC Name
Bacillus subtilis
  Synonym
Vibrio subtilis
  Lineage Kingdom: Bacteria
Phylum: Firmicutes
Class: Bacilli
Order: Bacillales
Family: Bacillaceae
Genus: Bacillus
  Oxygen Sensitivity
Facultative anaerobe
  Microbial Metabolism
Respiration; Fermentation of carbohydrates and central metabolism intermediates
  Gram
Positive
  Host Relationship
Probiotic
  Genome Size (bp)
4215606
  No. of Coding Genes
3940
  No. of Non-Coding Genes
121
  No. of Small Non-Coding Genes
121
  No. of Gene Transcripts
4061
  No. of Base Pairs
4263792
  Description
Bacillus subtilis, known also as the hay bacillus or grass bacillus, is a gram-positive, catalase-positive bacteria, found in soil and the gastrointestinal tract of ruminants and humans.
  External Links Taxonomy ID 1423
GutMDisorder ID gm0067
Genome Assembly ID ASM69118v1
GOLD Database ID Go0527396
GIMICA ID MIC00136

Full List of Metabolite(s) Produced by This MIC
     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 . [1]
Histone Biotinylation H2AK9 EM Info Jurkat cells IL-5 promoter . [1]
           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 [1]
DNA Hypermethylation Ccl3 EM Info Hippocampal cells promoter Bacterial meningitis [1]
           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 MLH1 EM Info Serum CpG site . [1]
DNA Methylation MGMT EM Info Serum CpG site . [1]
DNA Methylation p16 EM Info Serum CpG site . [1]
DNA Methylation Ccl3 EM Info Hippocampal cells Promoter . [1]
Histone Deacetylation Sirtuin 4 EM Info . . . [1]
miRNA miR-22-3p EM Info QGY-7703 cells . Normal [1]
miRNA miR-149-5p EM Info QGY-7703 cells . Normal [1]
miRNA miR-22-3p EM Info HL-7702 cells . Normal [1]
miRNA miR-149-5p EM Info HL-7702 cells . Normal [1]
           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 H4 EM Info Primary lymphocytes FXN Friedreich's ataxia [2], [3]
Histone Acetylation H3 EM Info Primary lymphocytes FXN Friedreich's ataxia [1], [4]
Histone Trimethylation H3K27 EM Info Primary lymphocytes FXN Friedreich's ataxia [1]
Histone Trimethylation H3K9 EM Info Primary lymphocytes FXN Friedreich's ataxia [1]
           Metabolite Name: Pantothenic acid (B5) 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 . . . [1], [4]
Histone Deacetylation Sirtuin 4 EM Info . . . [5], [1]
Histone Methylation HMT EM Info . . . [1], [4]
           Metabolite Name: Pyridoxine (B6) 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 . . . [5], [1]
Histone Acetylation Histone Acetylase (HAT) EM Info . . . [1], [6]
Histone Deacetylation Sirtuin 4 EM Info . . . [1], [7]
Histone Methylation HMT EM Info . . . [1], [8]
           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 IGF2 EM Info Peripheral blood leukocyte DMR2 MTHFR C677T polymorphism [1], [9]
DNA Methylation MTHFR EM Info Peripheral blood leukocyte north shore MTHFR 677TT genotype [1], [9]
DNA Methylation AGTR1 EM Info Peripheral blood leukocyte Promoter MTHFR C677T polymorphism [1], [10]
DNA Methylation LINE-1 EM Info Peripheral blood leukocyte CpG sites MTHFR 677TT genotype [1], [10]
DNA Methylation GNA12 EM Info Peripheral blood leukocyte Promoter MTHFR C677T polymorphism [1], [11]
DNA Methylation Zac1 EM Info . . . [1], [11]
Histone Methylation H3K4 EM Info MGC-803 cells LSD1 Gastric cancer [1], [10]
           Metabolite Name: Thiamine (B1) 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 . . . [1], [9]
Histone Deacetylation Sirtuin 4 EM Info . . . [5], [1]
Histone Methylation HMT EM Info . . . [1], [9]
           Metabolite Name: Vitamin K 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 . . . [5], [1]
Histone Acetylation Histone Acetylase (HAT) EM Info . . . [1], [12]
Histone Deacetylation Sirtuin 4 EM Info . . . [1], [12]
Histone Methylation HMT EM Info . . . [1], [12]


References
1 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.
2 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.
3 Biosynthesis of Vitamins by Probiotic Bacteria.
4 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.
5 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.
6 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.
7 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.
8 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.
9 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.
10 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.
11 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.
12 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.

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