Integrated molecular approaches for fermented food microbiome research

Abstract

Molecular technologies, including high-throughput sequencing, have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities have generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment-especially diet and nutrition-in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and, to a lesser extent, live microbes into the human gut. Here, we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarize the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.

Keywords: fermented foods; high-throughput sequencing; metabolomics; metagenomics; microbiome; transcriptomics.

Figure 1.

Schematic diagram of four methods of fermentation. (A) Spontaneous fermentation: For sauerkraut, cabbage is processed into small pieces. Salt is added at the ratio of 2% per weight of cabbage. This draws out moisture from the plant cells. The resulting mixture of cabbage, salt, and water is placed in a vessel and left to ferment for at least 5 days. The microbes present on the cabbage are mainly responsible for fermentation. (B) Simple starter: Many alcoholic beverages are produced using a simple starter, such as the yeast Saccharomyces cerevisiae. For beer, there are several important steps: malting, milling, mashing, lautering, boiling, fermenting, conditioning, filtering, and packaging. The simple starter, S.cerevisiae, is added to the wort after boiling, and then removed after fermentation by filtration. (C) Complex starter: For the production of certain cheese (e.g. cheddar), milk is innoculated with a multiple-strain (three to six strains) starter culture of known strains and rennet. These strains are typically lactic acid bacteria such as Lactococcus lactis subspecies cremoris and Lactococcus lactis subspecies lactis. (D) Undefined starter culture: Kombucha can be produced using a defined starter powder or using a kombucha ‘SCOBY’ (Symbiotic Colony Of Bacteria and Yeast). For the latter traditional method, a microbially produced SCOBY is added to sugary tea. Roughly 10% of the previous fermented kombucha is also added to the tea. The SCOBY and the added fermented kombucha contain an undefined community of bacteria and yeasts that ferment the tea over 7–14 days.

Figure 2.

A schematic workflow to determine the contribution of microbes to the development of flavour in fermented foods using omics approaches. (A) Fermented foods are sampled for microbiome and/or volatilome analysis (red arrows). (B) Metabolic reconstruction to predict what volatiles are produced by the microbiome (green arrows). (C) Correlation analysis is used to determine whether strains are linked to volatiles (blue arrows). (D) Statistical approaches are used to predict the volatilome of a food based on its strain-level composition (grey arrows). (E) The information obtained from at least one of these approaches is used to select starters with desirable (and predictable) properties (gold arrows).

Figure 3.

The effects of fermented foods on humans. Fermented foods are consumed and the components of the product (including microorganisms, metabolites, prebiotics, and proteins) could modulate the host gut microbiome, which consequently results in increased production of a metabolite. Subsequently, this metabolite could elicit an immune response and/or enter circulation. Alternatively, the components of the fermented foods themselves could cause this effect. Typically, the effect of consuming fermented foods is transient, but some effects (e.g. changes in the composition of the microbiota) may persist afterwards.