Demystification of fermented foods by omics technologies

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Microbial fermentation leading to the production of foods and beverages is an ancient bioprocess but still practices worldwide to date. Despite the great economic, cultural, and social values of fermented foods, only a small part of them is well understood; however, most of them are still in a mysterious state to a certain extent. In recent years, the emerging omics techniques have been actively applied to explore the mysteries of fermenting processes for fermented foods worldwide, which could provide a comprehensive perspective to track fermentation systems. This review summarized the application of different types of omics techniques in fermented-food research based on the recent representative studies and predicted that microbiomics and foodomics would be the two main trends in the research of fermented foods.

Introduction

Microbial fermentation is an important biotechnique used for long-term food preservation and flavored food processing, which converts substrates (mainly macromolecules such as carbohydrates, proteins, lipids, etc.) in raw materials into beneficial metabolites (organic acids, alcohols, amino acids, peptides, fatty acids, etc.) by inoculation of microorganisms for better nutritional composition, sensory, and functional properties 1••, 2, 3. Although microbial fermentation leading to the production of foods and beverages is an ancient technique, it is still commonly practiced worldwide to date, which is closely related to our daily lives, and even shapes the behaviors of locals. For example, Baijiu is an important element of Chinese table culture [4]. Grape wine serves a similar role in many western countries [5].

Despite the great economic, cultural, and social values of fermented foods, only a small part of them, such as beer, wine, yogurt, and so on, with clear fermentation strains and target products, are well understood, however, most of them are still in a mysterious state to a certain extent. The related research is restricted by the following factors if not all. 1) The fermentation is usually in an open system, and microorganisms in the environment may be involved. 2) Fermented foods are mostly initiated by natural inoculation, fermentation starter (Qu), artificially auxiliary strains, or in a pit rich in related microorganisms 6, 7. In the brewing process, lots of strains, including bacteria or fungi may be cooperatively involved. 3) Fermented foods have strong regional characteristics, and therefore, the research force is relatively scattered. 4) Due to commercial interests, some producers may not want to disclose the production details of fermented foods.

In recent years, omics techniques are being actively applied to the research of fermented foods, which could provide a comprehensive perspective to analyze the brewing process. Therefore, this review summarized the application of different types of omics techniques in fermented-food research based on the recent representative studies and predicted future research concerns.

Section snippets

Metagenomic sequencing could clarify the microbiota of fermentation niche

The complex microbiota and their dynamic changes hinder our understanding of the processes of many traditional fermentations, especially when unrecognized or unculturable microorganisms involve in the fermentation process. Metagenomic sequencing is a powerful approach to explore the taxonomic and functional diversity of microbial communities, including unculturable ones [8], which is commonly used in the research of fermented foods in recent years.

Collectively, the analysis is mainly divided

Genomics could promote the understanding of the inner driving force of fermentation

Genomics is defined as the study of the genome and its actions [19]. Production of many fermented foods such as wine, beer, vinegar, soy sauce, and red mold rice, mainly relies on one or several core strains at a certain stage or the whole stage of fermentation. The genome analysis of core strains has become a routine in addressing fermentation mechanisms and the recent examples are Weissella koreensis in kimchi fermentation [20], Aspergillus oryzae for brewing soy sauce, and so on [21], and

Transcriptomics or metatranscriptomics help to understand the active biological processes and pathways under particular conditions

Transcriptomics is the study of total transcripts in a single-species sample, while metatranscriptomics extends transcriptomics to study a microbial community or an environmental sample [31]. Transcriptomics or metatranscriptomics are commonly used in the research of fermentation microorganisms. First and foremost, they could be used to acquire the active biological processes and pathways of fermentation microorganisms under specific time and conditions. For example, metatranscriptomics was

Proteomics or metaproteomics reveal the actual operation of biological processes and functional properties of microbial communities or fermented foods

Proteomics is defined as the comprehensive analysis of proteins in a single-species sample, while metaproteomics extends proteomics to study a multispecies microbial community [39]. Proteomics could be used to study the biological processes of fermentation microorganisms under specific circumstances, such as the salt-tolerance mechanisms of T. halophilus [40] and L. plantarum [41], the flavor-formation mechanism of Aspergillus oryzae under osmotic conditions during soy sauce fermentation [42],

Metabolomics could reveal the material basis of fermented foods in nutrition, sensory, and function

Metabolomics defined as the comprehensive analysis of metabolites in a biological specimen [48], is being increasingly utilized in understanding the fermentation process of foods in the view of metabolite profiles. First, metabolomics is used to monitor the dynamic metabolic changes to reflect the fermentative behaviors of microorganisms, and the recent reference examples were performed in black glutinous rice wine [49], black tea [50], and Douchi [51]. Second, metabolomics is also widely used

Conclusion and future perspectives

Omics tools offer the opportunity to trace and characterize traditional fermented foods. In general, the omics research on fermented foods can be summarized into two main parts (Figure 1). One part is to study the behavior of fermentation microorganisms, which addresses the fermentation mechanism from genomics to transcriptomics to proteomics to metabolomics. The other part is to analyze the properties of fermented-food products, which addresses their nutrition, sensory, function, and safety by

Conflict of interest statement

There are no competing interests.

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

• of special interest

•• of outstanding interest.

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