Native synthetic microbial communities enhance zha-chili by boosting the fermentation capacity of indigenous microorganisms.

Fermented foods are a crucial part of the global diet, accounting for one-third of global food intake. Traditional fermented foods often rely on natural fermentation, leading to safety risks. The construction of synthetic microbial communities (SynComs) tailored for fermented foods is a key strategy to solve these issues. Here, we designed and constructed SynComs consisting of two bacterial and three fungal species, utilizing the study model of zha-chili. Using various high-throughput sequencing technologies, the dynamic alternations of microorganisms during the fermentation process were investigated, and the impact of SynComs on the fermentation process was evaluated. SynComs reduced fermentation time by approximately 15 d, increased flavor yields (8% for ethyl lactate and ethyl acetate), and greatly improved the quality of the zha-chili. Meanwhile, SynComs altered the succession of the fungal community so that Pichia became the dominant microorganism throughout the fermentation process, and the pattern of fungal community succession was brought closer to the null model. Metagenomic annotation results showed notable changes in functional genes, especially in glycoside hydrolases family. SynComs enhanced the positive correlations between indigenous microorganisms and flavor compounds while increasing other community microorganisms' contribution to flavor production. These findings provide a new approach to improve the quality of zha-chili and other traditional fermented foods through natural fermentations. We proposed that SynComs enhanced fermented foods by boosting the fermentation capacity of indigenous microorganisms.