The hidden diversity of food microbiomes

The microbial organisms living in food and food systems have a key role in food processing, quality, safety, and even in human health promotion. This review aims to summarize recent advancements in the characterization of novel species from metagenomics data, with a focus on their relevance for food microbiology. We discuss the generation of metagenome-assembled genomes, a crucial step that facilitates comparative genomic analyses and development of databases for taxonomic profiling and functional potential characterization. We also highlight how these approaches enable new applications in food science and examine the broader implications of these findings to better understand the interactions between food and human health. Finally, we present key challenges that need to be addressed to fully characterize the hidden diversity of food microbiomes and to exploit their potential for innovation in food science and health-related applications.