Details of Microbe Species (MIC)

General Information of MIC (ID: MC0043)
  MIC Name
Eubacterium limosum
  Synonym
Bacteroides limosus, Butyribacterium limosum, Butyribacterium rettgeri, Mycobacterium limosum
  Lineage Kingdom: Bacteria
Phylum: Firmicutes
Class: Clostridia
Order: Clostridiales
Family: Eubacteriaceae
Genus: Eubacterium
  Oxygen Sensitivity
Obligate anaerobe
  Microbial Metabolism
Saccharolytic; Fermentative
  Gram
Positive
  Host Relationship
Commensal
  No. of Base Pairs
4150332
  Description
Eubacteria limosum is the type species of the genus Eubacteria. Cells stain gram-positive, are nonmotile, and occur often with swollen ends. The anaerobic type strain grows autotrophically using H 2 + CO 2 or CO as carbon and energy source.
  External Links Taxonomy ID 1736
GutMDisorder ID gm0315
GOLD Database ID Go0119287
GIMICA ID MIC00576

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]
           Metabolite Name: Phenylbutyrate 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 D283-MED cells . . [1], [2]
Histone Acetylation H3 EM Info DAOY cells . . [3], [2]
Histone Acetylation H4 EM Info D283-MED cells . . [3], [2]
Histone Deacetylation HDAC EM Info . . . [1], [2]
     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 H4 EM Info Eosinophil cell Foxo3A promoter Asthma [4], [5]
Histone Acetylation H3K27 EM Info HepG2 cells FASN promoter Hypoxia [4], [2]
Histone Acetylation H3K56 EM Info HepG2 cells FASN promoter Hypoxia [4], [2]
Histone Acetylation H3K9 EM Info HepG2 cells LDHA promoter Hypoxia [6], [2]
Histone Acetylation H3K9 EM Info HepG2 cells ACACA promoter Hypoxia [7], [2]
Histone Acetylation H3K27 EM Info HepG2 cells LDHA promoter Hypoxia [8], [2]
Histone Deacetylation HDAC9 EM Info Eosinophil cell . Asthma [4], [5]
           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 . [9], [2]
DNA Demethylation POU5F1 EM Info iPS cells promoter . [1], [2]
Histone Acetylation H3 EM Info CD41T cells Foxo3A promoter . [5], [10]
Histone Crotonylation H3K9 EM Info KGN cells GPR43 . [1], [2]
Histone Deacetylation HDAC2 EM Info . . . [5], [10]
Histone Deacetylation HDAC1 EM Info . . . [5], [10]
miRNA miR-92a EM Info Colon cancer cells . Colon cancer [9], [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 H3K23 EM Info C2C12 cells Myod . [11], [2]
Histone Propionylation H3 EM Info Primary myocytes lysine 23 Health [7], [2]


References
1 Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia. Nat Commun. 2016 Jun 30;7:11960. doi: 10.1038/ncomms11960.
2 Eubacterium limosum ameliorates experimental colitis and metabolite of microbe attenuates colonic inflammatory action with increase of mucosal integrity World J Gastroenterol. 2006 Feb 21;12(7):1071-7. doi: 10.3748/wjg.v12.i7.1071.
3 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.
4 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.
5 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.
6 Crosstalk between the microbiome and epigenome: messages from bugs. J Biochem. 2018 Feb 1;163(2):105-112. doi: 10.1093/jb/mvx080.
7 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.
8 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.
9 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.
10 Phenylbutyrate and phenylacetate induce differentiation and inhibit proliferation of human medulloblastoma cells. Clin Cancer Res. 2004 Feb 1;10(3):1150-9. doi: 10.1158/1078-0432.ccr-0747-3.
11 Butyrate drives the acetylation of histone H3K9 to activate steroidogenesis through PPAR-gamma and PGC1-alpha pathways in ovarian granulosa cells. FASEB J. 2021 Feb;35(2):e21316. doi: 10.1096/fj.202000444R.

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