MIAOME: Human microbiome affect the host epigenome

Lidan Wang; Wei Zhang; Xianglu Wu; Xiao Liang; Lijie Cao; Jincheng Zhai; Yiyang Yang; Qiuxiao Chen; Hongqing Liu; Jun Zhang; Yubin Ding; Feng Zhu; Jing Tang

doi:10.1016/j.csbj.2022.05.024

MIAOME: Human microbiome affect the host epigenome

Comput Struct Biotechnol J. 2022 May 17:20:2455-2463. doi: 10.1016/j.csbj.2022.05.024. eCollection 2022.

Authors

Lidan Wang¹, Wei Zhang², Xianglu Wu³, Xiao Liang¹, Lijie Cao¹, Jincheng Zhai¹, Yiyang Yang¹, Qiuxiao Chen¹, Hongqing Liu¹, Jun Zhang¹, Yubin Ding³, Feng Zhu², Jing Tang^{1

3}

Affiliations

¹ School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China.
² College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
³ Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing 400016, China.

Abstract

Besides the genetic factors having tremendous influences on the regulations of the epigenome, the microenvironmental factors have recently gained extensive attention for their roles in affecting the host epigenome. There are three major types of microenvironmental factors: microbiota-derived metabolites (MDM), microbiota-derived components (MDC) and microbiota-secreted proteins (MSP). These factors can regulate host physiology by modifying host gene expression through the three highly interconnected epigenetic mechanisms (e.g. histone modifications, DNA modifications, and non-coding RNAs). However, no database was available to provide the comprehensive factors of these types. Herein, a database entitled 'Human Microbiome Affect The Host Epigenome (MIAOME)' was constructed. Based on the types of epigenetic modifications confirmed in the literature review, the MIAOME database captures 1068 (63 genus, 281 species, 707 strains, etc.) human microbes, 91 unique microbiota-derived metabolites & components (16 fatty acids, 10 bile acids, 10 phenolic compounds, 10 vitamins, 9 tryptophan metabolites, etc.) derived from 967 microbes; 50 microbes that secreted 40 proteins; 98 microbes that directly influence the host epigenetic modification, and provides 3 classifications of the epigenome, including (1) 4 types of DNA modifications, (2) 20 histone modifications and (3) 490 ncRNAs regulations, involved in 160 human diseases. All in all, MIAOME has compiled the information on the microenvironmental factors influence host epigenome through the scientific literature and biochemical databases, and allows the collective considerations among the different types of factors. It can be freely assessed without login requirement by all users at: http://miaome.idrblab.net/ttd/.

Keywords: EM, Epigenetic molecule; Epigenetic modification; HDACs, histone deacetylases; Host epigenome; Human microbiome; LPS, lipopolysaccharide; MDC, microbiota-derived components; MDM, microbiota-derived metabolites; MSP, microbiota-secreted proteins; Microbiota-derived metabolites; Microbiota-secreted proteins; miRNA, microRNA; ncRNAs, non-coding RNAs.