Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota

Abstract

Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.

Multispecies biofilms in fermentation: Biofilm formation, microbial interactions, and communication

“…Recently, some studies have achieved the identification of microbial metabolic activities in biofilms, the diagnosis of potential food pathogens, and sanitation monitoring of food processing equipment by using nanosensors (such as Au nanoclusters, vancomycin‐magnetic nanoclusters, and amphiphilic carbon quantum dots), which can transfer biochemical information into optical signals (Pu et al., 2021). CRISPR/Cas9, as a precise method of gene editing, has been applied to improve starter culture strains to promote food fermentation, and the CRISPR/Cas9 toolbox can be used to target specific DNA sequences, allowing applications by selectively clearing pathogenic or spoilage microbes (Mannaa et al., 2021). Future studies in the field will benefit from cutting‐edge detection methods.…”

Fermented Food in Asthma and Respiratory Allergies—Chance or Failure?

“…Natural or spontaneous fermentation depends on the autochthonous microorganisms that naturally occur in the raw substrate or processing environment, as is the case in the production of various fermented soy products, fermented cereals, and fermented vegetables. This method is also used in the manufacturing process of wine, beer, and some fermented sausages [ 11 , 14 , 15 ]. The second type of fermentation, often referred to as “culture dependent”, is a technique using specific starter cultures that can be either natural or selected commercially.…”

“…The second type of fermentation, often referred to as “culture dependent”, is a technique using specific starter cultures that can be either natural or selected commercially. The starter culture approach is broadly applicable, and is used for preparation of dairy products, cheese, fermented sausages, and soy products such as kombucha, tempeh, and natto [ 11 , 15 , 16 ]. One of the methods used in culture-dependent fermentation is “backslopping”, in which a small quantity of the previously fermented food is inserted into raw food to start the new fermentation step.…”

“…One of the methods used in culture-dependent fermentation is “backslopping”, in which a small quantity of the previously fermented food is inserted into raw food to start the new fermentation step. Backslopping is commonly applied in the production of sauerkraut, sourdough bread, and certain fermented soy products [ 7 , 11 , 15 ] ( Table 1 ).…”

Two Faces of Fermented Foods—The Benefits and Threats of Its Consumption

“…The predominance of native microbiota allows limiting the growth of undesirable strains or species of microorganisms, as well as to reducing the toxic compounds they produce, ensuring the food safety. In developed countries, fermentation with the use of starter cultures also aims to achieve new health goals ( Hesseltine and Wang, 1980 ; Holzapfel, 1997 ; Tamang et al, 2016 , 2020 ; Voidarou et al, 2020 ; Mannaa et al, 2021 ). Research aimed at improving the starter cultures properties, carried out using the innovative CRISPR/Cas9 technology (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) which allows modification of the genome of any microorganism, may play an essential role here ( Wu et al, 2020 ; Vilela, 2021 ).…”