Eagle Genomics helps uncover impact of everyday consumer products on our microbiome using AI
Ever wondered what the blizzard of chemicals we come into contact with daily is doing to you?
From detergents to skin creams, and from the food we eat to the toothpaste we use, there is growing interest in the impact everyday consumer products have on our natural biology.
In particular, companies are increasingly keen to find out the effect on our microbiota – the collection of trillions of micro-organisms that live within us.
Has our obsession with hygiene actually proved, well, unhygienic? Are we destroying the friendly microbes that we need to function normally with our highly efficient antibacterial agents?
And how is our health and wellbeing being affected by the changes we induce to the bacteria, viruses, fungi and single-celled organisms known as archaea with which we share our bodies?
Disruption to this microbial environment is being implicated in a whole host of conditions, from inflammatory bowel syndrome to metabolic diseases, cancer and Parkinson’s.
The study of the microbiome – technically the combined genetic material of our microbiota, but the two words are often used interchangeably – is an explodng field.
“It’s a new dawn,” says Eagle Genomics CEO Anthony Finbow, whose company has just secured a $3.5million investment led by the Environmental Technologies Fund to develop further its artificial intelligence-powered platform for analysing microbiome data.
“We are starting to see the beginnings of this science and I think it’s going to have a major impact on our understanding of health, wellness and illness.”
Each day seems to bring a new revelation.
One recent study published in the Microbiome journal found evidence that the length of time a child was breastfed, and his or her pre-school diet, continued to have an impact on the gut microbiota into the school years.
And this month scientists at the Wellcome Sanger Institute and EMBL’s European Bioinformatics Institute, both in Hinxton, and Hudson Institute of Medical Research in Australia announced they had uncovered 100 new species of bacteria in healthy human intestines by studying human faeces.
One previously unthinkable medical procedure – the faecal transplant – has now become a proven method for treating chronic Clostridium difficile infections. Taking a healthy stool, screening it for anything dangerous, and transplanting it into a sick patient can help reintroduce the vital friendly gut flora destroyed by antibiotics, which allowed the C.diff microbes to take hold in the first place.
(If you’re eating your lunch, feel free to skip this paragraph but, for the curious, both a ‘bottom-up’ procedure using a fresh, donated stool blended with saline and ‘top-down’ method employing a frozen sample through a nose tube can be used. Some patients, struggling to find a clinic willing to perform the procedure, have even turned to DIY transplants from loved ones. Meanwhile, work goes on to produce a poo-in-a-pill, or crapsule, if you’ll excuse the phrase, that could do the same job without destroying your blender.)
For all its potential though, study of the microbiome currently seems to raise more questions than answers. With more of the cells we harbour being microbial than human, how do we begin to make sense of them?
From its base at the BioData Innovation Centre on the Wellcome Genome Campus in Hinxton, Eagle Genomics is helping companies to find some answers. It has also been selected to join the Microsoft AI Factory accelerator programme at the renowned Station F start-up campus in Paris.
“We are providing the tools, the platforms, the mechanism to enable the scientists to engage with their data, have a conversation with the data and to discover new insights,” Anthony tells the Cambridge Independent. “In this market, people make aggressive claims around the microbiome and how their products might help or improve the microbiome. What is required is that these claims can be substantiated.
“Particularly in the health and wellbeing space, there is a lot of noise about probiotics, prebiotics and skin microbiome-friendly treatments.
“The reality is it is very difficult to demonstrate the science to prove the claims. That’s what is most exciting for us.”
Eagle Genomics’ knowledge discovery platform, the e[automateddatascientist] deploys artificial intelligence, machine learning and data science to analyse complex genomic and microbiomic data at scale.
The aim is to enable companies to assess the viability, efficacy and safety of their products.
“We’ve helped our major client, Unilever, launch a toothpaste product called Zendium based on scientific, marketable claims that have been generated through utlisation of our platform,” says Anthony.
“They’ve done comprehensive studies and clinical trials to prove that the product helps the oral microbiome and they’ve done that in part on our platform.
“That’s the first documented use of a scientific claim around the microbiome for a personal care product.”
Although not yet on sale here via retailers, it is available via Amazon and other online stores.
Promising to ‘boost your good bacteria’, while reducing ‘the bad bacteria that cause dental problems’, Zendium is said to ‘protect your mouth naturally with natural enzymes and proteins’.
“This is just the beginning,” says Anthony. “The oral microbiome is one route into the body. The gut microbiome is still largely undiscovered. The skin microbiome is a major theme for the cosmetics industry – it’s described as the number one marketing theme in that realm this year.”
According to Anthony, the science is evolving fastest in areas driven by “the consumer products companies, in the personal care, food and cosmetics space, and of course in the agritech space, where the soil microbiome is being decimated because of the way we are treating the soil”.
He adds: “Our objective is to build our platform to enable the science in these realms and then in the next phase address the opportunity of solving illness.”
Huge quantities of data are being generated in the pursuit of understanding how products impact the microbiome.
“We are providing the mechanism and platform to ingest, curate, catalogue and navigate those data and then enable the exploratory data analysis.
“Perhaps 20-30 per cent of the data is the customers’ own proprietary experimentation processes but they are looking increasingly to capture third party external data, perhaps from contract research organisations, and sequencing companies are generating microbiome DNA data,” says Anthony. “We are providing the mechanism and platform to ingest, curate, catalogue and navigate those data and then enable the exploratory data analysis.
“The research and development paradigm is changing. These companies are looking to explore open innovation processes – such as ‘I’ve got this question, is there anyone out there with data who is interested in a conversation?’.
“We are going to enable that because at the root of our platform is a valuation technology that enables matching of questions to data.
“That is going to enable the data-orientated, digital reinvention of life sciences R&D.”
The US-based global management consultancy McKinsey described digital in research and development as a $100billion market opportunity over the next decade.
And our microbiome is like a newly-discovered human organ.
So there is little wonder that Eagle Genomics is attracting major interest. Last year, it announced a partnership with Microsoft Genomics, marking Microsoft’s first venture into the microbiome.
“That’s what is such a tremendous, exciting opportunity,” says Anthony. “It changes the whole context for our understanding of health and wellness.
“Before, the germ theory of disease was suggesting bacteria are the enemy, the immune system is the defence mechanism and we need to kill them. If you look all around your house and all the products are marketed on the basis that they kill 99.9 per cent of bacterial.
“That’s based on the germ theory of diseases. We’re now moving beyond what is called the hygiene hypothesis at the other end of the spectrum. Depriving ourselves of these microbes is possibly the root of a whole range of non-communicable diseases – auto-immmune conditions, inflammatory diseases, obesity, asthma, possibly even autism being implicated as a result of the damage to the microbial environment
“I think it’s the beginning of a new dawn and it’s tremendously exciting to be at the forefront, but also actually selling products to address the challenge today.”
Professor Ian Charles, director of the new Quadram Institute in Norwich, agrees.
He spoke at the OBN BioTuesday event, What's New in Microbiome Research, at Babraham on February 12, about the importance of the microbiome when considering future healthcare opportunities.
“The gut microbiome is now believed to play a significant role in a number of diverse medical conditions from IBD to dementia. Quadram Institute research is at the forefront of the interface between food, gut biology and health, and we are applying new multi-omic analyses to move research beyond correlation and into causation,” he told the Cambridge Independent.
Among the other companies at the forefront of microbiome research is Eagle Genomics' neighbour Microbiotica, which won Life Sciences Company of the Year at the 2018 Cambridge Independent Science and Technology Awards.
It is helping to match a patient’s bacteria to function, and developing medicines and biomarkers based on microbiota.
Isabelle de Cremoux, CEO and managing partner of Seventure Partners, which is investing in Microbiotica, said: “The microbiome is now one of the hottest areas for healthcare investment and, with scientific understanding being advanced at a rapid pace, it is becoming clear that the microbiome will play a key role in the treatment of a whole host of diseases.
“I foresee a great year ahead for our focused microbiome fund, Health for Life Capital. We see huge potential in the UK, including in Cambridge, and were pleased to have invested in Hinxton-based Microbiotica last year. We look forward to an exciting year of progress.”