Understanding The Health Benefits Of Fermented Foods

EU-funded researchers have developed an affordable data analysis toolbox for finding and interpreting the genomic sequence of fermented food – the key to better understanding their potential benefits and risks.

Cheese, yoghurt, bread and wine. Besides being regular staples of the human diet, these all share one thing in common: they are fermented foods. As fermented food, they are produced from raw materials like milk, fruits and cereals via the activity of such microorganisms as yeast and lactic acid bacteria.

We already know that sometimes the foods generated by microorganisms come with significant health benefits. When they do, these particular microorganisms are called ‘probiotic’ strains. Less well known is the exact nature of these health benefits. This is because a microorganism’s functional potential is determined by its genomic sequence, which is where its enzymes and proteins are encoded.

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To better understand the potential health benefits of a probiotic strain, scientists need to not only determine what the genomic sequence is, but also be able to interpret that sequence. For this, specific tools must first be developed.

This is where GENOBOX enters the picture, creating value from all the data being generated through genomic sequencing of microorganisms used in the food industry, according to project coordinator Wynand Alkema. “These genomic sequences harbour clues with respect to the pathogenicity, toxicity and capacity for spoilage, and on possible beneficial properties of the organism.”

The properties include everything from an organism’s capacity to add flavour and texture to a food, to inducing such health benefits as weight loss and improved gastro-intestinal health.

Clearing the hurdle to access

It is extremely difficult to handle the massive amounts of data generated during sequencing, and to transform them into actionable knowledge – especially for SMEs. To do this requires specific IT infrastructure and personnel skilled in bioinformatics and data analytics. For many European SMEs, this is simply a hurdle too big to overcome, thus preventing them from capitalising on this wealth of data.

To help clear this hurdle, the GENOBOX project worked as a consortium of SMEs, academia and experts from the dairy and probiotic industry, who together created a toolbox in which genomic analysis can be used for predicting the functional properties of microorganisms. With this toolbox, industry can determine the specific functional benefits of bacterial species in a fast, cost-efficient and easily repeated manner. With this information in hand, they can then design effective, multi-species probiotic mixtures and select promising strains for use in food fermentation.

Translating data into predictions

“Typically, determining the functionality and performance of a bacterial strain using standard experimentation can be time-consuming, complex and expensive,” says Alkema.

Although numerous companies are already sequencing their industrial strains, what the GENOBOX project brings to the table is an innovative way to translate this genomic data into strain functionality traits, including yield, probiotic properties, safety, and production of flavour compounds.

“By using a specialist bioinformatics infrastructure and expertise to develop, manage and interpret this data, the toolbox or ‘GENOBOX’ can predict the functional properties of bacterial strains based solely on their genomic sequencing and compare this data with hundreds of genomes of microorganisms available in the public domain,” explains Alkema.

To conduct these predictions, the GENOBOX server contains a substantial number of predictive models, all based on known genes with a known function and relationship with phenotypic properties. Matching the predictive models to the genome sequence for individual organisms yields the phenotypic predictions.

According to Alkema, all of the project’s IT infrastructure and algorithms are disseminated via a website, from which the genome sequences of microorganisms can be analysed in a simple, fast and interactive way.

“This means that companies no longer have to carry out elaborate and expensive experiments, but can directly assess whether their microorganism has potential health benefits or confers a risk as a food spoiler based on the genomic sequence, which can be produced at a fraction of the costs it would normally take to carry out this type of experimental work,” concludes Alkema. “This is extremely helpful for SMEs.”