Microbial function in food fermentations: Current research and future directions.

Complex microorganisms are the drivers of fermentation ecosystem and play a pivotal role in determining product yield and quality. Although significant efforts have been devoted to characterizing microbial composition and diversity, these cannot fully elucidate microbial functions that are critical to the fermentation process and product quality. There is an urgent need to shift research focus toward microbial function, particularly those closely associated with food flavor, texture, quality, and nutrition. Currently, function prediction based on amplicon sequencing and omics techniques remain the predominant strategies for investigating microbial function in food fermentations. However, these methods generate population-averaged data, masking functional heterogeneity, rare taxa, and key contributors within low-abundance populations. Emerging technologies, stable-isotope probing and single-cell sequencing offer promising alternatives. This review provides an overview of methods for investigating microbial function in food fermentations, spanning conventional to emerging techniques, while critically assessing their respective advantages and limitations. Additionally, we summarize recent research in microbial functions in fermented foods. By providing methodological insights and future perspectives, this review aims to guide targeted research on microbial function in complex fermentation systems.