Meta-omics insights in the microbial community profiling and functional characterization of fermented foods

•Meta-omic analyses explore the underlying mechanism of food fermentation.•Meta-omics reveal valuable genes and bioactive substances in fermented foods.•Integrated meta-omics are promising for function exploration and production practice.

BackgroundFood fermentation is an important pillar of societal traditions, but also crucial in terms of economy for numerous regional products, as well as rich microbiological resources awaiting exploration. During the past few years, tremendous efforts have been made to provide important and deeper insights into the underlying molecular mechanisms of fermented foods through amplicon analysis, metagenomic and metatranscriptomic sequencing, as well as metaproteomic investigation, and integrated with metabolomics analysis.Scope and approachIn this review the meta-omic tools applied in fermented foods are summarized. Then the recent meta-omic studies in cheese, vinegar, fermented alcoholic beverage, fermented vegetables, fermented tea, and soybean products are reviewed and emphasized.Key findings and conclusionsMainly based on high-throughput DNA sequencing, amplicon analysis, metagenomics and metatranscriptomics, together with metaproteomics and high-resolution metabolomics have allowed exploration of microbial community dynamics and functional characterization in traditional fermented foods in astonishing scale and speed during the past few years. The recent applications of meta-omics in cheese, vinegar, fermented alcoholic beverage, fermented vegetables, fermented tea, and soybean products explore the underlying mechanism of food fermentation and reveal fermented foods as rich sources of valuable genes and bioactive substances. Though there is limitation, promising clues exist for future investigation. Further integration of multiple meta-omic tools, together with powerful statistical analysis methods will assuredly lead to more detailed functional characterization and more efficient and sustainable production practices in fermented foods worldwide.