Details of Microbe Species (MIC)

General Information of MIC (ID: MC0693)
  MIC Name
Pseudomonas nitroreducens HBP1
  Synonym
Pseudomonas azelaica HBP1, Pseudomonas nitroreducens DSM 8897, Pseudomonas sp. DSM 8897, Pseudomonas sp.
  Lineage Kingdom: Bacteria
Phylum: Proteobacteria
Class: Gammaproteobacteria
Order: Pseudomonadales
Family: Pseudomonadaceae
Genus: Pseudomonas
  Oxygen Sensitivity
Aerobe
  Microbial Metabolism
Respiratory
  Gram
Negative
  Genome Size (bp)
7408198
  Description
Pseudomonas nitroreducens HBP1 is a gram-negative and aerobic strain from the genus of Pseudomonas.
  External Links Taxonomy ID 1437882
GOLD Database ID Go0075305

Full List of Metabolite(s) Produced by This MIC
     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], [2]
DNA Demethylation POU5F1 EM Info iPS cells promoter . [1], [2]
Histone Acetylation H3K9 EM Info KGN cells GPR41 . [1], [2]
Histone Acetylation H3K9 EM Info KGN cells GPR43 . [1], [2]
Histone Acetylation H3 EM Info CD41T cells Foxo3A promoter . [3], [1]
Histone Deacetylation HDAC2 EM Info . . . [4], [1]
Histone Deacetylation HDAC1 EM Info . . . [4], [1]
miRNA miR-92a EM Info Colon cancer cells . Colon cancer [3], [1]
           Metabolite Name: Lactate 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
miRNA miR-141-3P EM Info Oral epithelial cells . Autistic spectrum disorder [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 H3K23 EM Info C2C12 cells Myod . [5], [1]
Histone Propionylation H3 EM Info Primary myocytes lysine 23 Health [1], [6]
     Molecule Type: Other metabolites
           Metabolite Name: a-Ketoglutarate (a-Kg) 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 Trimethylation H3K27 EM Info Mesenchymal stromal stem cells Nanog promoter Age-related osteoporosis [7], [1]
Histone Trimethylation H3K9 EM Info Mesenchymal stromal stem cells Nanog promoter Age-related osteoporosis [7], [1]
Histone Trimethylation H3K27 EM Info Mesenchymal stromal stem cells Bmp4 promoter Age-related osteoporosis [8], [1]
Histone Trimethylation H3K27 EM Info Mesenchymal stromal stem cells Bmp2 promoter Age-related osteoporosis [1], [6]
Histone Trimethylation H3K9 EM Info Mesenchymal stromal stem cells Bmp2 promoter Age-related osteoporosis [9], [1]


References
1 The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992.
2 Alpha-ketoglutarate ameliorates age-related osteoporosis via regulating histone methylations. Nat Commun. 2020 Nov 5;11(1):5596. doi: 10.1038/s41467-020-19360-1.
3 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.
4 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.
5 Potential Associations Among Alteration of Salivary miRNAs, Saliva Microbiome Structure, and Cognitive Impairments in Autistic Children. Int J Mol Sci. 2020 Aug 27;21(17):6203. doi: 10.3390/ijms21176203.
6 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.
7 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.
8 Crosstalk between the microbiome and epigenome: messages from bugs. J Biochem. 2018 Feb 1;163(2):105-112. doi: 10.1093/jb/mvx080.
9 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.

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