Dark Matter: The New Science of the Microbiome

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Eat more omega 3 New research suggests a relationship between gut microbes, omega 3 and brain health In 2023, looking after the gut has become a popular pastime for the health-conscious. And for good reason. According to Cancer Research, Bowel cancer is now the fourth most common cancer in the UK, yet 54 per cent of cases are preventable. One condition for which IMT has proven safe and effective is recurrent C. difficile infection (rCDI), a bacterial infection of the gastrointestinal tract that can sometimes lead to multi-organ failure and death. Even though antibiotics are an effective therapy for CDI, there is a risk of the antibiotics not working, or of patients having further recurrence of the condition once the antibiotics are finished, according to Dr Benjamin Mullish, a clinician and lecturer in Imperial’s Department of Metabolism, Digestion and Reproduction. If you want to get rid of C. difficile infection, a more effective strategy is to restore the composition and function of your gut microbiome to how it was before you became ill. Dr Benjamin Mullish Department of Metabolism, Digestion and Reproduction Consultant surgeon, Dr. James Kinross, is Senior Lecturer in Colorectal Surgery in the Department of Surgery & Cancer at Imperial College London. He is also a consultant surgeon at Imperial College Healthcare NHS Trust. His research interests include how the gut microbiome causes colorectal (bowel) cancer, how we can influence it to improve our health and the use of artificial intelligence for real-time decision support in the operating theater.

How would this understanding of the host-chemotherapeutic microbiota axis help us to formulate cancer treatment therapies in the future? I try to reduce the amount of meat that I eat. In fact, I almost never eat meat unless someone else is cooking,” he says. Instead, Dr Kinross focuses on eating a range of vegetables. “I try to have at least 30 different fruits and vegetables a week and I try to make sure that every meal I have is vegetable-based. We have a lot of salads in my house, and we love our polyphenols.”His research interests include how the gut microbiome causes colorectal (bowel) cancer, how we can influence it to improve our health and the use of artificial intelligence for real-time decision support in the operating theatre. Dr Kinross’ is also an active researcher with interests spanning three NIHR BRC themes- Digestive Diseases, Surgery and Cancer and Infection and AMR. Kinross J. Translational applications of the oncological microbiome in clinical practice. Stellenbosch University Microbiome Meeting. Stellenbosch, South Africa. November 2019 Dr James Kinross is a consultant surgeon at Imperial College Healthcare NHS Trust and senior lecturer in colorectal surgery in the Department of Surgery & Cancer at Imperial College London. His research interests include how the gut microbiome causes colorectal (bowel) cancer, how we can influence it to improve our health and the use of artificial intelligence for real-time decision support in the operating theatre. A microbiome refers to all the microscopic organisms within a particular environment and all of the things that they need to sustain themselves. They exist at lots of different scales and we have them all around, on and inside us. So, for example, our planet has a microbiome and we have microbiomes on our skin, in our lungs and in our gut. Our microbiomes have evolved with us and they change and grow with us over our lifetime. They have an important symbiotic role in our health: they need us to survive, but we need them too. The products EnteroBiotix is developing are a very interesting experimental tool. By studying whether it works, we can learn about the microbiome and the very specific mechanisms that make microbiome treatments work. We could produce drugs for or leverage for biomarkers. Then we can refine it so we can deliver at scale for organisations like the NHS. That’s the company’s mission and it aligns with ours.” The Imperial team is a discovery engine and EnteroBiotix can help translate that into a commercial product that benefits patients around the world. Dr James McIlroy EnteroBiotix

There is currently a big programme of work trying to develop automated processes for the deployment of this technology in the microbiology lab because it takes seconds to get data as opposed to days if we were using traditional culturing techniques. There are also clinical trials to ascertain whether we could do things like measuring the gut microbiome during endoscopy. Dr James Kinross is a Senior Lecturer in Colorectal Surgery and a Consultant Surgeon at Imperial College London. We caught up with him to find out more about his career and research…One of the first collaborations between Imperial and EnteroBiotix is on a project trialling the potential for IMT administered to patients with blood cancer prior to bone marrow transplant as a means of trying to alter their gut microbiome and try and improve outcomes. He was awarded a Royal College of Surgeons of England training fellowship during his PhD and he was funded by the Academy of Medical Sciences as an early stage lecturer. He is a visiting professor at the Royal College of Surgeons of Ireland and is currently funded by Bowel and Cancer Research and the NIHR Imperial Biomedical Research Centre. We need to better understand an individual’s individual ecology, both before and after treatment. If we can do this, it may mean we can more effectively target treatment stratify therapy. The key thing about the gut microbiome is that it is modifiable and the strategic shift is towards a “drugable microbiome” i.e. we make drugs to target the bacteria in the gut rather than the host. So, you may not need to change the therapy but you could change the microbiome and there are a number of different ways in which we could potentially do that. For example, one interesting avenue that is being studied a lot at the moment is looking at how we could utilise faecal microbial transplantation in modifying the gut microbiome. However, this is quite a blunt tool, and we may be able to give highly selected commensal strains engineered to produce the molecular candidates we need. This is likely to be a very important role for probiotics in the future. If you change their diet to one that is high in fat and protein but low in fibre, you see dramatic changes in the functions of the microbes that exist within their gut. These changes cause and drive inflammation and we think this increases the risk of cancer and other chronic diseases. What should we do to protect our gut microbiome?