How using network science creates opportunities in the era of ‘multi-omics’ [Interview]

While microbial data can yield significant innovation opportunities, interpreting the sheer amount of information available can prove challenging. What’s more, traditional scientific practices do not always give the full picture.

Eagle Genomics is pioneering a fresh approach to science that could revolutionise how industries approach innovation. By collecting populations of data and examining the networks between them, the TechBio company aims to achieve a more holistic understanding of biological systems.

“This is not biotech; rather, we are about applying technology to elucidate biology,” explains Yvonne Pinto, director of bioeconomy at Eagle Genomics, and who will be speaking with her colleague Bram Goorden, COO, at Vitafoods 2023.

“Network science is about looking at populations of data by applying deep science. It’s not traditional science - looking at just one microbe and its interaction with a host - it is about looking at a range of microbes and examining the metabolites they produce, other interactions etc. This is what helps us to understand the whole system.”

Focus on microbes

Eagle Genomics aims to use its tech-driven data approach to drive sustainable change across a range of issues that impact human, animal and planetary wellbeing. This is what the company calls its ‘one health agenda’. A key focus is on microbes, because of their importance to life and their potential in finding sustainable solutions to global challenges.

“This includes finding solutions to inflammatory diseases and metabolic health,” says Pinto. “These issues can be addressed by functional foods and natural ingredients. Microbes also have a role to play in soil and plant health, regenerative agriculture and combating antibiotic resistance. They condition the availability of nutrients to plants, the adaption of plants to stress, and facilitate the nutrient content of plants. Microbes enable sustainable life on earth in all manner of ways.”

Microbes are in our food system – in pre- and probiotics and fermented foods for example – and exist in our gut. Scientists are continually finding out more about the health benefits of a healthy microbiome, with growing evidence of links to mental health and prevention of non-communicable diseases. Everything is connected.

“We also know that the microbiome regulates our ability to respond to therapeutics,” says Pinto. “We could, for example, manipulate the microbiome to tip us into ‘responder’ mode.”

Making data-driven innovation available

Eagle Genetics has developed a cloud-based software platform, and works with companies interested in identifying underlying microbial mechanisms, how they function, and what potential applications might exist.

Networks of associations between big datasets - on multi-omic biomarkers for nutrients, pre, pro-biotics and post-biotics for example - are examined using deep learning. In the past, such data might have been siloed. The platform also enables the integration of public data sources with proprietary data sources.

“The initial data are often proprietary to our customer, but we saw an opportunity to combine these with other datasets in ways that we never could do previously. This is why the deep science aspect is so important – our teams understand the underlying questions which drive the need for insights of our customers. We think the potential applications are huge and what drives us is the ‘one health’ agenda,” says Goorden.

Eagle Genomics has helped major brands to deliver a range of microbiome-benefiting products including an enzyme-based toothpaste that retains oral microbiome health, and provided evidence for claims on microbiome-friendly products and novel ingredients in various industries, such as agritech, nutrition, and human health. Partners also include standards organisations and technology partners.

Ultimately, Pinto, Goorden and their colleagues believe that to transform our global food system, we need to focus on how we provide nutrition to both humans and animals. And given the role that microbes play in conditioning the nutrient quality of our food, this should be a key area of focus.

Pinto and Goorden will be delivering a presentation at Vitafoods 2023 entitled ‘Delivering new data architecture in the microbiome for the multi-omics era’.