Microbiome data science’s key role in next-generation food products


Advances in microbiome-based data science and technology—including AI-based analytics and the mainstream accessibility of powerful computer processing—will play a key role as next-generation food producers look to accelerate our understanding of nutrition and health.

Microbiome data science’s key role in next-generation food products

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Malnutrition isn’t a problem experienced exclusively in developing countries. Intensive farming, overuse of chemicals in the soil and antibiotics in the food chain, over-emphasis on the taste and calorific content of foods, and a preference for convenience and processed products have left even the richest nations under-nourished. This, in turn, is having a detrimental effect on public health.

Immunity issues, food intolerances, and allergies are at an all-time high and, in the wake of Covid-19, stakeholders from across multiple sectors are demonstrating a renewed interest in wellness and the notion of “food as medicine.” Food manufacturers, supply-chain partners, and agricultural innovators are now joined by governments and food safety agencies in promoting more nutritious diets and investigating foods which work in harmony with the gut to promote a more robust and naturally supported immune system. This effort requires not only addressing the soil crops are grown in, and the feeds, treatments, and conditions provided to animals, but also the constituents of foods.

It is in this context that the microbiome—the interactions and effects of different combinations of microbes (in this case on the health of the human “host”)—has come into sharper focus, especially now that sophisticated technology exists to allow the microbiome to be analyzed in conjunction with a wide range of other scientific data. For food and nutrition R&D organizations, this opportunity is hugely exciting. For the first time, it offers the means to create, test, and demonstrate the efficacy of new products which work symbiotically with the human body to create better health outcomes.

Holistic Food Solutions

Heightened public consciousness has become sensitive to all kinds of food-related issues, which government taskforces are seeking to reflect in food safety standards and policy, and which food and nutrition companies are trying to respond to with new waves of product innovation. Food production is being looked at as a whole. There is an emerging consensus that meat and dairy substitutes, for example, must be created with consideration of the planet and rainforests, while also offering nutritional benefits to the consumer. It is no good solving one problem (with alternative proteins), only to create another (environmental destruction or diminished health outcomes). The plant-based food brand Beyond Meat has embodied this thinking with new product choices which allow the consumer to choose a healthier or “taste-first” option.

The microbiome also plays a role in holistic food solutions. Attention to the microbiome—which more broadly encompasses the soil and what is fed to animals, as well as what goes into the human body—offers a way forward for next-generation food producers. A slew of innovative startup companies have cottoned onto this quickly, ready to disrupt the market with new products that promote robust human health by working in harmony with and improving the body’s natural state.

In response to this, major food brands must transform their own portfolios to keep pace with these newcomers, and with growing consciousness about the nutritional content of the food people are ingesting. Cargill in the U.S. and Unilever, Royal DSM, and Sofina/Danone in Europe are among those innovating with micro-ingredients and micronutrients to deliver new generations of food products.

The Microbiome Is Big Business

Bill Gates, the co-founder of Microsoft and now a philanthropist and advocate for global health transformation, maintains that understanding the microbiome will be “as big a breakthrough as anything else we will do in health over the next two decades.”

It isn’t just the food industry that is taking note of this, either. Innovators in pharma/biotech have a keen interest in the interactions of drugs with the microbiome and how this might be optimized in the future to transform health outcomes. A report1 published by the McKinsey Global Institute in May 2020 suggests that many trillions of dollars of business opportunity in life sciences alone could be unlocked with a greater understanding of the microbiome.

“Agritech” companies are interested in how they might enrich the soil or improve animal feeds at the start of the food chain. And cosmetics and personal care innovators are looking at how future products might be made safer, more beneficial, and less costly to the environment by harnessing and working with existing host conditions (such as toothpastes that work with or improve the microbial environment in the mouth).

Advances in Microbiome-Based Data Science

To capitalize on the numerous opportunities here, companies first need to understand the role of the microorganisms and their interactions both with each other and with the active ingredients of their products. This, in turn, relies on the ability to be able to combine and cross-analyze a lot of different biological data and reliably interpret any correlations.

Until now, this critical dimension—microbial data science—has been missing from disease/wellness/product modeling, holding companies back from optimizing their products or being able to scientifically claim their benefits for the proper working of the gut and the immune system. There are still some practical hurdles to overcome—for example, around data standardization. Yet, advances in technology—especially graph databases, AI-based analytics, and the mainstream accessibility of powerful computer processing—are allowing everyone from product R&D organizations to food safety regulators to benefit from meaningful microbiome-based knowledge discovery and analytics and distill credible scientific evidence that can be applied safely to advance product innovation.

Within the next decade, there will be a much deeper understanding of the microbiome, thanks to the availability of techniques and mechanisms that make it possible to understand the data in a way that hasn’t been possible before. This will facilitate powerful new discoveries about nutrition and health and move the industry towards a secure and sustainable solution to feeding and improving the health of multiplying populations far into the future.

Anthony Finbow is CEO at Eagle Genomics. The company, headquartered in Cambridge, UK, is a pioneer in applying network science—particularly linked to the microbiome—to biology. Its award-winning, trademarked AI-augmented knowledge discovery and analytics platform, e[datascientist], helps companies looking to innovate with next-generation food, personal care, cosmetics, and agritech products, supported by science. The platform harnesses the latest graph technology and Microsoft’s advanced machine learning and cognitive services.


  1. McKinsey Global Institute report. “The Bio Revolution: Innovations Transforming Economies, Societies, and Our Lives.” Published May 13, 2020. Accessed here.

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