Challenges and perspectives of quantitative microbiome profiling in food fermentations

Abstract

Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.

Keywords:

• Food fermentation
• microbiota
• process control
• quantitative microbiome profiling

Disclosure statement

The authors declare that there is no conflict of interest regarding the publication of this article.

Additional information

Funding

This work is financially supported by the National Natural Science Foundation of China (32172175), Key R&D Program of Guangxi Province (AA21077004), National First-Class Discipline Program of Light Industry Technology and Engineering (LITE2018-12), the Priority Academic Program Development of Jiangsu Higher Education Institutions, the 111 Project (No. 111-2-06).