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Artificial intelligence fuels the mega-trend of microbiome research

Artificial intelligence is connecting the dots of cross-sectoral microbiome research and helping farm-to-fork businesses advance towards science-backed health claims.

Understanding the microbiome – the populations of bacteria, viruses and fungi that coexist in our bodies and the environment around us – is a mammoth task because of the sheer complexity of the data. This is further compounded by researchers working in siloes as well as varieties in experimental methods and standards, which mean results cannot be compared.

Cambridge-headquartered Eagle Genomics says it has developed an Artificial Intelligence-powered platform called e[datascientist] that navigates these data, creating visual representations and making it easier to find novel relationships between different data points. This is paving the way for a greater understanding of the microbiome, it says.

“We started the business on the outside, addressing the human microbiome on the external realm – the skin – and now we are going inwards,” said CEO of the company, Anthony Finbow. “The gut microbiome is such a huge and extraordinary opportunity. It presents unprecedented challenges in terms of accessibility of data, and we really know so little about it. In the same way as we go deep into the oceans and discover brand new species, we are just at the beginning of the journey to understand what is in the gut microbiome.”

Interconnected: Healthy animals, people and planet

Finbow sees elements of a vicious circle operating at the heart of the modern food system.

Contemporary farming practices, such as monocultures, tilling, and a reliance on chemical fertilizers are depleting essential bacteria from soil. This limits the nutrient uptake of the plants grown in that soil while limited dietary diversity is reducing the microbial diversity in the gut. Just five crops, rice, maize, wheat, millet and sorghum provide 60% of the world's food energy intake, according to the Food and Agriculture Organization (FAO).

Microbiome research has the potential to address some of these problems, and manufacturers are beginning to take note.

This year, the start-up inked a multi-year deal with the world’s biggest food company, Cargill, which will use its e[datascientist] platform to understand the association between the microbiome and digestive and immune health in humans and animals.

“Healthy animals, healthy people and a healthy planet are all interconnected," said Mike Johnson, marketing director at Cargill Health Technologies, at the time of the announcement.

Eagle Genomics also works with a major poultry supplier to see if its birds are healthy, are being fed appropriately, and if their microbiome profiles indicate dangerous pathogens that could cause a foodborne illness outbreak. The poultry producer commissions third party firms to collect data on its operations and then analyses these data using the Eagle Genomics platform.

“Fundamentally, all these companies are trying to do the same thing; understand whether their products do good or harm, and to ensure that they do good; this could be skin products, hair cream, deodorant, or food,” Finbow told Fi Global Insights.

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‘Robust, repeatable, traceable’

In a narrow sense, the microbiome can be thought of as a bioreactor in the gut that transforms what individuals eat into what they need to subsist; “the software that programmes your immune system”, said Finbow.

There are hundreds more genes in the gut micro-organisms than the human genome, and these genes are responsible for programming the production and development of metabolites, proteins, and other materials that the human body cannot do on its own.

Interest in the microbiome and food that promotes gut health is on the rise. Previously unknown products such as kefir and kombucha now line supermarket shelves and in 2019, European consumers bought probiotic supplements, probiotic yoghurt and sour milk products worth $10.2 billion in 2019, according to the International Probiotics Association (IPA).

However, there are still no approved probiotic health claims in Europe; to date, businesses have submitted more than 350 probiotic claims to the European Food Safety Authority (EFSA) for approval, all of which have been rejected.

Although challenging, Finbow said this regulatory environment is stimulating its work.

“To make microbiome-specific product claims is going to be a very difficult thing [and] the regulator will be scrutinising ever more aggressively. Because […] we are talking about therapeutic outcomes and, crudely speaking, food as medicine, we will see the same regulatory challenge as in the biotech and pharma space.

“We are enabling [manufacturers] to make robust, repeatable, traceable, and explicable scientific claims so that they can differentiate or personalise their products based on science.”

Immune health

Finbow believes the microbiome is the nexus between food and immune health.

“I definitely see this as a mega trend and the COVID-19 challenge has focused attention even more on health and wellness. We see a huge correlation between obesity or metabolic health and susceptibility to COVID symptoms and […] because of microbiome dysbiosis, damage to the microbiome, our immune systems are no longer programmed effectively; they are out of tune, and [there is] a huge, exponential rise in auto-immune challenges and susceptibility to illness as a function of that.”

In the past five years, Europe has led the world with the most immunity-enhancing product launches (41%) in the food, drink and healthcare category, according to market research company Mintel, which predicts this trend will continue, exemplified by fears over coronavirus.

“The immunity trend is not a blip,” said Rick Miller, associate director of specialised nutrition at Mintel during a recent Fi Global Insights webinar on the impact of the COVID-19 pandemic on demand for health and wellness ingredients.

“It’s going to get stronger and keep growing, at least until we get a COVID-19 vaccine. The lack of a vaccine encourages experimentation. Consumers will look elsewhere. People will make their own faith and belief system. Food and drink that can support the immune system is one big area of interest for European consumers,” he said.

TAGS: Trends
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