Details of Microbe Species (MIC)

General Information of MIC (ID: MC0035)
  MIC Name
Desulfovibrio piger
  Synonym
Desulfomonas pigra Moore
  Lineage Kingdom: Bacteria
Phylum: Proteobacteria
Class: Deltaproteobacteria
Order: Desulfovibrionales
Family: Desulfovibrionaceae
Genus: Desulfovibrio
  Gram
Negative
  No. of Coding Genes
2535
  No. of Non-Coding Genes
97
  No. of Small Non-Coding Genes
97
  No. of Gene Transcripts
2632
  Description
Desulfovibrio piger is an SRB from the Proteobacteria phylum (deltaproteobacteria) and formerly known as Desulfomonas pigra, is a gram-negative, nonmotile, rod-shaped bacteria.
  External Links Taxonomy ID 901
Genome Assembly ID DESPIGER

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 H4 EM Info Eosinophil cell Foxo3A promoter Asthma [1], [2]
Histone Acetylation H3K9 EM Info HepG2 cells LDHA promoter Hypoxia [3], [2]
Histone Acetylation H3K9 EM Info HepG2 cells ACACA promoter Hypoxia [4], [5]
Histone Acetylation H3K56 EM Info HepG2 cells FASN promoter Hypoxia [6], [5]
Histone Acetylation H3K27 EM Info HepG2 cells FASN promoter Hypoxia [7], [5]
Histone Acetylation H3K27 EM Info HepG2 cells LDHA promoter Hypoxia [8], [2]
Histone Deacetylation HDAC9 EM Info Eosinophil cell . Asthma [1], [2]
           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 . [9], [2]
Histone Acetylation H3 EM Info CD41T cells Foxo3A promoter . [10], [5]
Histone Crotonylation H3K9 EM Info KGN cells GPR43 . [9], [2]
Histone Deacetylation HDAC2 EM Info . . . [11], [2]
Histone Deacetylation HDAC1 EM Info . . . [11], [2]
miRNA miR-92a EM Info Colon cancer cells . Colon cancer [12], [5]
     Molecule Type: Other metabolites
           Metabolite Name: Hydrogen sulfide (H2S) 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 Foxp3 EM Info Treg cells Promoter Adoptive transfer colitis [13], [5]
DNA Methylation DNMT3A EM Info Smooth muscle cells . . [14], [5]
DNA Methylation TFAM EM Info Smooth muscle cells promoter: 210 bp and30 bp . [14], [5]
DNA Methylation AT1b EM Info Inflammatory cells Genbank:U01033 277-1454 Hypertension [15], [2]
DNA Methylation DNMT1 EM Info HUVECs . . [16], [2]
Histone Acetylation H3 EM Info THP-1 cells IL-6 promoter Inflammation [17], [5]
Histone Acetylation H3 EM Info THP-1 cells TNF-Alpha promoter Inflammation [17], [5]
Histone Deacetylation HDAC EM Info THP-1 cells . Inflammation [17], [5]
Histone Deacetylation SIRT3 EM Info Cardiomyocytes . Myocardial hypertrophy [18], [5]
Histone Deacetylation SIRT1 EM Info A549 cells . Mitochondrial dysfunction [9], [2]
Histone Methylation H3K27 EM Info THP-1 cells IL-6 promoter Inflammation [17], [5]
Histone Methylation H3K27 EM Info THP-1 cells TNF-Alpha promoter Inflammation [17], [5]
Histone Methylation H3K9 EM Info THP-1 cells IL-6 promoter Inflammation [17], [5]
Histone Methylation H3K9 EM Info THP-1 cells TNF-Alpha promoter Inflammation [17], [5]
miRNA miR-194 EM Info Glomerular endothelial cells . Genetic diabetic kidney [19], [5]
miRNA miR-129 EM Info Glomerular endothelial cells . Hypertension [18], [5]
miRNA miR-455 EM Info BEAS-2B cells . Hypoxic injury [9], [2]
miRNA miR-126-3p EM Info HUVECs . . [16], [2]


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 Lactate-utilizing community is associated with gut microbiota dysbiosis in colicky infants Sci Rep. 2017 Sep 11;7(1):11176. doi: 10.1038/s41598-017-11509-1.
3 Crosstalk between the microbiome and epigenome: messages from bugs. J Biochem. 2018 Feb 1;163(2):105-112. doi: 10.1093/jb/mvx080.
4 Hydrogen sulfide signaling in regulation of cell behaviors. Nitric Oxide. 2020 Oct 1;103:9-19. doi: 10.1016/j.niox.2020.07.002. Epub 2020 Jul 17.
5 Hydrogen Sulfide and Sulfate Prebiotic Stimulates the Secretion of GLP-1 and Improves Glycemia in Male Mice Endocrinology. 2017 Oct 1;158(10):3416-3425. doi: 10.1210/en.2017-00391.
6 Involvement of miR-455 in the protective effect of H(2)S against chemical hypoxia-induced injury in BEAS-2B cells. Pathol Res Pract. 2018 Nov;214(11):1804-1810. doi: 10.1016/j.prp.2018.08.008. Epub 2018 Aug 16.
7 Hydrogen sulfide attenuates mitochondrial dysfunction-induced cellular senescence and apoptosis in alveolar epithelial cells by upregulating sirtuin 1. Aging (Albany NY). 2019 Dec 23;11(24):11844-11864. doi: 10.18632/aging.102454. Epub 2019 Dec 23.
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 Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia. Nat Commun. 2016 Jun 30;7:11960. doi: 10.1038/ncomms11960.
10 Hydrogen sulfide alleviates hypertensive kidney dysfunction through an epigenetic mechanism. Am J Physiol Heart Circ Physiol. 2017 May 1;312(5):H874-H885. doi: 10.1152/ajpheart.00637.2016. Epub 2017 Feb 17.
11 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.
12 GYY4137, a Hydrogen Sulfide Donor Modulates miR194-Dependent Collagen Realignment in Diabetic Kidney. Sci Rep. 2017 Sep 7;7(1):10924. doi: 10.1038/s41598-017-11256-3.
13 Hydrogen Sulfide Promotes Tet1- and Tet2-Mediated Foxp3 Demethylation to Drive Regulatory T Cell Differentiation and Maintain Immune Homeostasis. Immunity. 2015 Aug 18;43(2):251-63. doi: 10.1016/j.immuni.2015.07.017. Epub 2015 Aug 11.
14 Hydrogen Sulfide Maintains Mitochondrial DNA Replication via Demethylation of TFAM. Antioxid Redox Signal. 2015 Sep 1;23(7):630-42. doi: 10.1089/ars.2014.6186. Epub 2015 May 14.
15 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.
16 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.
17 Hydrogen sulfide attenuates cytokine production through the modulation of chromatin remodeling. Int J Mol Med. 2015 Jun;35(6):1741-6. doi: 10.3892/ijmm.2015.2176. Epub 2015 Apr 8.
18 Hydrogen sulfide rescues high glucose-induced migration dysfunction in HUVECs by upregulating miR-126-3p. Am J Physiol Cell Physiol. 2020 May 1;318(5):C857-C869. doi: 10.1152/ajpcell.00406.2019. Epub 2020 Mar 18.
19 Maternal Renovascular Hypertensive Rats Treatment With Hydrogen Sulfide Increased the Methylation of AT1b Gene in Offspring. Am J Hypertens. 2017 Nov 6;30(12):1220-1227. doi: 10.1093/ajh/hpx124.

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