Microbiota of foods: a comprehensive review of diversity and potential implications

Microbial communities play a central role in food ecosystems. Fermented foods, in particular, host complex and dynamic microbiomes that are shaped by raw materials, fermentation substrates, processing environments, and regional production practices. This review provides an in-depth analysis of microbial diversity in various spontaneously fermented food products, including beverages, dairy products, and ethnic and other traditional food products. It highlights how microbial composition evolves throughout fermentation and how specific microorganisms contribute to the safety and sensory profiles of the final products. The field has undergone a methodological transformation, moving from classical culture-based methods to advanced omics technologies. Culture-independent approaches such as metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metabolomics enable a more comprehensive characterization of microbial communities, providing insights not only into their taxonomic composition but also into their functional roles. Despite increasing interest in metagenomics and metatranscriptomics, metataxonomic high-throughput sequencing, particularly 16S rRNA and ITS gene analyses, remains the most widely used technique due to its lower cost and accessibility. However, it provides limited resolution at the species level and cannot distinguish between live and dead cells. Microbiome characterization using omics has practical implications for the food industry, including the identification of microbial signatures in artisanal foods and the improvement of understanding fermentation processes. Our manuscript emphasizes a broad comparative overview of microbial diversity across multiple categories of fermented foods and integrates this with a methodological perspective on omics approaches used to characterize these communities. Findings outline the main methodological approaches, sequencing platforms, primer sets, and bioinformatic tools used in studies, as well as the current limitations and future directions in the field. Integrative multi-omics strategies are expected to significantly enhance food safety, quality, traceability, and functionality across diverse food systems.