MetaMed Overview

Metagenomics Medicine mapping system (MetaMed), is a novel and integrative system-wide correlation mapping system to link bacteria functions and medicine therapeutics. In this system, a well-defined similarity score between microbial metabolite entity and medicine entity is applied to link microbiota functions and existed medicine therapeutics. We demonstrate with comprehensive and solid evidence that such a linking strategy, although straightforward while never tried before, can help to achieve accurate predictions of microbial effects on human body. The key idea behind MetaMed is to use a well-defined similarity score to measure the similarity between the metabolites derived from microbe biosynthetic gene clusters (BGCs ) and public available drugs. We leverage KEGG pathway annotations to justify our proposed MetaMed score schema, and our score can be applied to identify metabolites with potential therapeutic effects effectively. By using such a scoring system, MetaMed integrates the microbe and public medicine information from MIBiG , DrugBank , LINCS , SIDER etc., providing a comprehensive data source for the deeply investigation of the microbe impact on human body by linking the microbe metabolites to the functions of known drugs, resulting in a systematic mapping system of MetaMed including the links of microbe-drug, microbe-treatment indication, microbe-side effect and microbe-immune status transition etc. The aim of our study is to present a novel computational strategy to decipher microbial effect on human health, we validate the identified relationships with literature evidences. Future experimental validation and investigations are encouraged to perform on these derived hypotheses or predicted results.

1. MetaMed allows to search or browse the microbe BGC and their related metabolites information!
2. MetaMed allows to search or browse the microbe’s potential side effects on human body!
3. MetaMed allows to search or browse the equivalent drugs with certain functional and structure similarity scores to the given microbe metabolites!
4. MetaMed allows to search or browse the impact of microbe on immune status transition by the defined score system, providing useful clues for personalized microbe-based immune-therapy!
5. MetaMed provides a user-friendly data preprocessing pipeline, Metapipe to process the personalized human microbe sequencing data (WGS or 16s rRNA) to obtain the personalized human BGC profile!
Version Info
MetaMed alpha version: 2017-3-15
MetaMed release version 1.0: 2017-6-1,
with 15000+ inner tests
MetaMed release version 1.1: 2018-01-24,
MetaMed release version 1.2: 2019-01-2,
MetaMed release version 1.3: 2019-07-2,

Feel free to contact:

Han Zhao, Tongji University Send Mail
Qi Liu, Tongji University Send Mail

MetaMed: Linking microbiota functions with medicine therapeutics, Han Zhao, Qi Liu et al, submitted, 2019