Niche Construction: A Rational Engineering Strategy for Regulating Microbial Assembly to Enhance Flavor and Bioactivity of Fermented Foods

Microbial communities serve as metabolic engines that determine the flavor and bioactivity of traditional fermented foods. Nonetheless, the stochastic nature of spontaneous fermentation often leads to niche uncertainty, resulting in inconsistent product quality and unstable functional expression. Transitioning traditional, empirically driven fermentation processes into precisely controllable modern biomanufacturing systems therefore requires an urgent paradigm shift from passive observation to active ecological engineering. In this review, we propose niche construction as a core strategy for the directional manipulation of microbial community assembly. We systematically examine the major dimensions of ecological niches in fermentation systems, including resource, environmental, spatial, and biotic niches, and further discuss how their temporal dynamics regulate microbial community assembly through dispersal, selection, ecological drift, and diversification. In addition, we assess specific engineering strategies based on niche construction, including the precise design of raw material substrates and the dynamic feedback regulation of fermentation parameters. Niche construction can reduce assembly stochasticity by guiding microorganisms from the occupation of available realized niches toward the expression of desired functional niches, thereby stabilizing flavor formation, bioactive metabolite production, and safety-related functions. Looking ahead, we explore the integration of artificial intelligence with multi-omics approaches for real-time niche prediction and the use of 3D printing to create spatially structured substrates, thereby enabling the precise manipulation of microbial spatial niches.