MIAOME: Human microbiome affect the host epigenome

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 metabol...

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Main Authors: 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
Format: Article
Language:English
Published: Elsevier 2022-01-01
Series:Computational and Structural Biotechnology Journal
Subjects:
Online Access:http://www.sciencedirect.com/science/article/pii/S2001037022001805
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author 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
author_facet 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
author_sort Lidan Wang
collection DOAJ
description 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/
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spelling doaj.art-8ab255b2475c4934930987f199e1aba92022-12-24T04:52:30ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012024552463MIAOME: Human microbiome affect the host epigenomeLidan Wang0Wei Zhang1Xianglu Wu2Xiao Liang3Lijie Cao4Jincheng Zhai5Yiyang Yang6Qiuxiao Chen7Hongqing Liu8Jun Zhang9Yubin Ding10Feng Zhu11Jing Tang12School of Basic Medicine, Chongqing Medical University, Chongqing 400016, ChinaCollege of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, ChinaJoint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing 400016, ChinaSchool of Basic Medicine, Chongqing Medical University, Chongqing 400016, ChinaSchool of Basic Medicine, Chongqing Medical University, Chongqing 400016, ChinaSchool of Basic Medicine, Chongqing Medical University, Chongqing 400016, ChinaSchool of Basic Medicine, Chongqing Medical University, Chongqing 400016, ChinaSchool of Basic Medicine, Chongqing Medical University, Chongqing 400016, ChinaSchool of Basic Medicine, Chongqing Medical University, Chongqing 400016, ChinaSchool of Basic Medicine, Chongqing Medical University, Chongqing 400016, ChinaJoint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing 400016, China; Corresponding authors at: School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China (J. Tang).College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Corresponding authors at: School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China (J. Tang).School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing 400016, China; Corresponding authors at: School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China (J. Tang).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/http://www.sciencedirect.com/science/article/pii/S2001037022001805Human microbiomeHost epigenomeEpigenetic modificationMicrobiota-derived metabolitesMicrobiota-secreted proteins
spellingShingle 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
MIAOME: Human microbiome affect the host epigenome
Computational and Structural Biotechnology Journal
Human microbiome
Host epigenome
Epigenetic modification
Microbiota-derived metabolites
Microbiota-secreted proteins
title MIAOME: Human microbiome affect the host epigenome
title_full MIAOME: Human microbiome affect the host epigenome
title_fullStr MIAOME: Human microbiome affect the host epigenome
title_full_unstemmed MIAOME: Human microbiome affect the host epigenome
title_short MIAOME: Human microbiome affect the host epigenome
title_sort miaome human microbiome affect the host epigenome
topic Human microbiome
Host epigenome
Epigenetic modification
Microbiota-derived metabolites
Microbiota-secreted proteins
url http://www.sciencedirect.com/science/article/pii/S2001037022001805
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