Details of Microbe Species (MIC)

General Information of MIC (ID: MC0723)
  MIC Name
Clostridium difficile
  Synonym
Bacillus difficilis
  Lineage Kingdom: Bacteria
Phylum: Firmicutes
Class: Clostridia
Order: Clostridiales
Family: Peptostreptococcaceae
Genus: Clostridioides
  Oxygen Sensitivity
Obligate anaerobe
  Microbial Metabolism
Fermentative
  Gram
Positive
  Host Relationship
Opportunistic pathogen
  Genome Size (bp)
4167076
  No. of Coding Genes
3815
  No. of Non-Coding Genes
83
  No. of Small Non-Coding Genes
83
  No. of Gene Transcripts
3898
  No. of Base Pairs
4268322
  Description
Clostridioides difficile is a species of gram-positive, anaerobic bacteria from the genus Clostridioides.
  External Links Taxonomy ID 1496
GutMDisorder ID gm0200
Genome Assembly ID ASM331356v1
GOLD Database ID Go0508393
GIMICA ID MIC00396

Full List of Metabolite(s) Produced by This MIC
     Molecule Type: Amino acid (AAs)
           Metabolite Name: Phenylacetate 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 Deacetylation HDAC EM Info . . . [1], [2]
     Molecule Type: Fatty acids
           Metabolite Name: Butyrate 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
DNA Demethylation DPPA2 EM Info iPS cells promoter . [1]
DNA Demethylation POU5F1 EM Info iPS cells promoter . [1]
Histone Acetylation H3 EM Info CD41T cells Foxo3A promoter . [1]
Histone Deacetylation HDAC2 EM Info . . . [1]
Histone Deacetylation HDAC1 EM Info . . . [1]
miRNA miR-92a EM Info Colon cancer cells . Colon cancer [1]
     Molecule Type: Phenolic compounds
           Metabolite Name: Benzoate 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 Benzoylation H3K4 EM Info HepG2 cells TKbzQTAR (modified peptide) . [3], [4]
Histone Benzoylation H4K12 EM Info HepG2 cells GLGKbzGGAKacR (modified peptide) . [3], [5]
Histone Benzoylation H4K16 EM Info HepG2 cells GGKprGLGKprGGAKbzR (modified peptide) . [3], [5]
Histone Benzoylation H3K9 EM Info HepG2 cells KbzSTGGKacAPR (modified peptide) . [1]
Histone Benzoylation H2BK5 EM Info HepG2 cells PEPTKbzSAPAPK (modified peptide) . [1]
Histone Benzoylation H3K14 EM Info HepG2 cells STGGKbzAPR (modified peptide) . [1]
Histone Benzoylation H3K18 EM Info HepG2 cells KbzQLATKacAAR (modified peptide) . [1]
Histone Benzoylation H3K23 EM Info HepG2 cells KQLATKbzAAR (modified peptide) . [1]
Histone Benzoylation H4K5 EM Info HepG2 cells GKbzGGKacGLGKacGGAKacR (modified peptide) . [1]
Histone Benzoylation H4K8 EM Info HepG2 cells GKacGGKbzGLGKacGGAKacR (modified peptide) . [1]
Histone Benzoylation H2BK11 EM Info HepG2 cells SAPAPKbzK (modified peptide) . [1]
Histone Benzoylation H2BK16 EM Info HepG2 cells KbzAVTKacAQK(modified peptide) . [1]
Histone Benzoylation H2BK20 EM Info HepG2 cells KAVTKbzAQK(modified peptide) . [1]
Histone Benzoylation H2AK13 EM Info HepG2 cells AKbzAKprSR (modified peptide) . [1]
Histone Benzoylation H2AK9 EM Info HepG2 cells GKacQGGKbzAR (modified peptide) . [1]
           Metabolite Name: Hydroxicinnamic acid 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 . . . [1]
Histone Acetylation Histone Acetylase (HAT) EM Info . . . [6], [5]
Histone Methylation HMT EM Info . . . [7], [5]
           Metabolite Name: Hydroxybenzaldehyde 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 . . . [1], [8]
           Metabolite Name: Hydroxycoumarin 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 Deacetylation HDAC1 EM Info Epithelial cells Nrf2 promoter . [1], [2]
           Metabolite Name: Hydroxyphenylacetic 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 . . . [1], [2]
Histone Deacetylation HDAC EM Info . . . [1], [2]
           Metabolite Name: Hydroxyphenylpentanoic acid 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 . . . [1], [2]
Histone Deacetylation HDAC EM Info . . . [1], [2]
Histone Methylation HMT EM Info . . . [1], [2]
           Metabolite Name: Hydroxyphenylpropanoic acid 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 . . . [1], [2]
Histone Acetylation Histone Acetylase (HAT) EM Info . . . [1], [2]
Histone Deacetylation HDAC EM Info . . . [1], [2]
Histone Methylation HMT EM Info . . . [1], [2]
           Metabolite Name: P-cresol 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], [2]
Histone Deacetylation HDAC EM Info . . . [1], [2]
Histone Methylation HMT EM Info . . . [1], [2]
           Metabolite Name: Valerolactone 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 . . . [1], [2]
Histone Deacetylation HDAC EM Info . . . [9], [5]
Histone Methylation HMT EM Info . . . [9], [5]


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 Lysine benzoylation is a histone mark regulated by SIRT2. Nat Commun. 2018 Aug 28;9(1):3374. doi: 10.1038/s41467-018-05567-w.
3 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.
4 p-Cresyl Sulfate. Toxins (Basel). 2017 Jan 29;9(2):52. doi: 10.3390/toxins9020052.
5 Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria PLoS Pathog. 2018 Sep 12;14(9):e1007191. doi: 10.1371/journal.ppat.1007191. eCollection 2018 Sep.
6 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.
7 Crosstalk between the microbiome and epigenome: messages from bugs. J Biochem. 2018 Feb 1;163(2):105-112. doi: 10.1093/jb/mvx080.
8 7-Hydroxycoumarin Attenuates Colistin-Induced Kidney Injury in Mice Through the Decreased Level of Histone Deacetylase 1 and the Activation of Nrf2 Signaling Pathway. Front Pharmacol. 2020 Jul 28;11:1146. doi: 10.3389/fphar.2020.01146. eCollection 2020.
9 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.

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