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Related Experiment Video

Updated: Sep 20, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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MIAOME: Human microbiome affect the host epigenome.

Lidan Wang1, Wei Zhang2, Xianglu Wu3

  • 1School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China.

Computational and Structural Biotechnology Journal
|June 6, 2022
PubMed
Summary

The Human Microbiome Affect The Host Epigenome (MIAOME) database compiles microenvironmental factors influencing host epigenetics. It details microbes, metabolites, and epigenetic modifications linked to 160 human diseases.

Keywords:
EM, Epigenetic moleculeEpigenetic modificationHDACs, histone deacetylasesHost epigenomeHuman microbiomeLPS, lipopolysaccharideMDC, microbiota-derived componentsMDM, microbiota-derived metabolitesMSP, microbiota-secreted proteinsMicrobiota-derived metabolitesMicrobiota-secreted proteinsmiRNA, microRNAncRNAs, non-coding RNAs

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Area of Science:

  • Microbiome research
  • Epigenetics
  • Computational biology

Background:

  • Microenvironmental factors significantly impact host epigenome regulation.
  • Microbiota-derived metabolites (MDM), components (MDC), and secreted proteins (MSP) are key factors.
  • Existing literature lacked a centralized database for these factors and their epigenetic links.

Purpose of the Study:

  • To construct a comprehensive database, MIAOME, detailing microenvironmental factors affecting the host epigenome.
  • To consolidate information on microbes, their derived factors, and epigenetic modifications.
  • To facilitate research on the interplay between the microbiome and host epigenetics in human diseases.

Main Methods:

  • Literature review and integration of data from scientific literature and biochemical databases.
  • Systematic curation of information on human microbes, microbiota-derived metabolites/components, and secreted proteins.
  • Classification of epigenetic modifications including DNA modifications, histone modifications, and non-coding RNAs.

Main Results:

  • The MIAOME database includes 1068 human microbes, 91 microbiota-derived metabolites/components from 967 microbes, and 40 proteins from 50 microbes.
  • It identifies 98 microbes directly influencing host epigenetic modifications.
  • The database categorizes 4 DNA modifications, 20 histone modifications, and 490 non-coding RNA regulations linked to 160 human diseases.

Conclusions:

  • MIAOME provides a unified resource for understanding microenvironmental influences on the host epigenome.
  • The database enables collective consideration of various factors affecting host epigenetics.
  • MIAOME is freely accessible, supporting research into microbiome-epigenome interactions and associated diseases.