Comprehensive Large-Scale Integrative Analysis of Omics Data To Accelerate Specialized Metabolite Discovery

Microbial specialized metabolites are key mediators in host-microbiome interactions. Most of the chemical space produced by the microbiome currently remains unexplored and uncharacterized. This situation calls for new and improved methods to exploit the growing publicly available genomic and metabolomic data sets and connect the outcomes to structural and functional knowledge inferred from transcriptomics and proteomics experiments. Here, we first describe currently available approaches that support the comprehensive mining of metabolomics and genomics data. Next, we provide our vision on how to move forward toward the automated linking of omics data of specialized metabolites to their structures, biosynthesis pathways, producers, and functions.

Automated summary

Microbial specialized metabolites play a crucial role in host-microbiome interactions, and there is a need for new methods to utilize the expanding genomic and metabolomic datasets while connecting them to structural and functional knowledge inferred from transcriptomics and proteomics experiments. This article describes current approaches for comprehensive mining of metabolomics and genomics data, as well as proposes a vision for automated linking of omics data of specialized metabolites to their structures, biosynthesis pathways, producers, and functions.