Dark Matter: The New Science of the Microbiome

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Ideally, we need to nurture our gut microbiome from birth. I think that this is so important, that it should be a given human right. One of the ways to do this is for women to breastfeed if they can and for children to have all their vaccinations – that way, they’re much less likely to need antibiotics. When used correctly, antibiotics save lives, but overuse causes more harm than good. We also need our children to play outside with other children and to have a diverse diet that is high in fibre and low in saturated fats. Have you made changes in your own life because of what you’ve learnt about our gut microbiome? He performs clinical trials using intra-operative mass spectrometry (known as the iKnife) for improving the precision of the surgical treatment of colorectal cancer. He also studies the role of the gut microbiome in the aetiology of colon cancer, Crohn’s disease and obesity. How well do you know your gut? You may have seen the word probiotics on your food, or possibly seen recipes to help your gut health with the three K’s: Kombucha, Kefir and Kimchi. But if your life depended on it, would you eat someone else’s poo?

An urgent investigation into the brave new world of the microbiome and how it shapes our lives and health. 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.” 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. The partnership between Imperial and EnteroBiotix, in addition to helping explore the safety, tolerability and efficacy of IMT based drugs for a range of conditions, is expected to help place microbiome research onto a more systematic footing. This trial will exploit another important advantage of the capsules, namely that their components are manufactured in a very standardised way, which is both better for patient safety, and allows researchers to start exploring the specific mechanisms as to how IMT may beneficially impact upon patients’ immune system and other aspects of their health. By studying these tools, we can learn about the microbiome and the very specific mechanisms that make microbiome treatments work. Dr James Kinross Department of Surgery & CancerI knew the gut microbiome was important to our health and I wanted to focus my future career on understanding how": Meet James Kinross

That tells us that although these bugs seem to come up time and time again in literature, they are probably not necessarily causative. That doesn’t necessarily mean they’re not valid targets for developing novel therapies for treating colon cancer, but it just means that if you’re trying to prevent cancer, they may not be the best targets. Eat more fibre Most of us eat only half the recommended 30g a day. But start slowly – our guts don’t like rapid change 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 and 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. Why is the gut microbiome important? Kinross J. The Digital Surgeon. Association of Colorectal and Proctological Surgery. Edinburgh, September 2020.There are lots of confusing pieces of dietary advice for people as to what to eat,” says Dr Kinross. “Of course, it needs to be tailored a little bit depending on your health and your goal but generally, you’ve got to put more fibre into the gut. That’s the key message from me.” We all know from epidemiological studies what a healthy diet for the gut looks like. The microbiome is the critical mediator that determines whether our diet is going to be good or bad for us and therefore this poses the question whether we can engineer the microbiome so that we can get the very best out of the diet we’re consuming. Or could we possibly supplement with secondary metabolites that may have some benefit? Pre-habilitation’ prior to a significant medical intervention isn’t new – one example is getting leaner and fitter, which is often recommended before major surgery,” says Professor Marchesi. “But it’s a new idea in the context of patients having bone marrow transplants, and definitely very novel to be targeting the gut microbiome as a means to pre-habilitate patients. At the moment, we just have correlations, but with this new trial we can start exploring cause and effect.” With dazzling science and fascinating stories spanning from the dawn of humankind to the current race to develop personalised healthcare, and practical advice on how to nurture your microbiome through your diet and lifestyle, this pioneering book will change the way you think about human health forever.

Nicholson JK, Holmes E, Kinross JM, Darzi AW, Takats Z, Lindon JC: Metabolic phenotyping in clinical and surgical environments. Nature 2012, 491(7424):384-392. The study will be run across six of the UK’s leading blood cancer centres and includes, along with Imperial, UCLH, The Royal Marsden, King’s College London, Leeds Teaching Hospitals, and University Hospitals Birmingham. Advancing microbiome researchEverything we’re doing now is scratching the surface,” says Spector. “We are maybe 10% of the way there, because every week, we’re discovering something new. Humans want an easy answer [to improve our gut health], but you shouldn’t take anyone seriously who doesn’t say it’s complicated,” he says. “There’s a massive industry that needs a simple message to sell its products. They want to say all you’ve got to do is eat this bar, this yoghurt or this protein drink.” How would this understanding of the host-chemotherapeutic microbiota axis help us to formulate cancer treatment therapies in the future?

Dr James Kinross was trained in northwest London, and was a National Institute for Health Research clinical lecturer in surgery, and an Ethicon laparoscopic fellow in colorectal surgery. The scale of the task is immense. The bacteria in the gut alone weigh close to 1.5 kg, they’re made up of about 100,000,000,000,000 bacterial cells (that’s 100 trillion) – equivalent in number to the total number of cells that make up the human body – and they speak millions of different molecular languages. Another major challenge in studying the microbiome is its physical distribution. The micro- biome is dispersed across our bodies in different niches, each with varying total abundances of microbes. Being clear about our anatomical definitions is important. 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.The human microbiome represents the most important new therapeutic target that we have for treating the greatest threats to human life in the 21st century and for preventing future pandemics of pathogens. This was not only important for Ray – it is critical for all of us: without a stable and diverse microbiome, we may well lose our minds. Behind all this is a simple message: microbes are not the enemy. There’s a lot of science in the book to support my hypothesis. It’s for anyone who is interested in how we can improve our health and who wants to understand why we get disease and how to prevent it, so I have tried to make it easy to understand. Dr James Kinross a Consultant surgeon specialising in the gut microbiome at Imperial College London and Imperial College Healthcare NHS Trust has published a new book, Dark Matter. the book explains the role of micro-organisms in our bodies and the impact on our health of their imbalance in our system and the world around us. In his new book Dark Matter: The New Science of the Microbiome, Dr James Kinross lays bare the mind-boggling world of what lies in our guts: the delicate ecosystem of trillions of microbial life forms that live within us all. Without us even realising, our gut’s unique ecosystem is the missing link in modern medicine and what’s more, is heavily influenced by our environment. Our gut microbiome is responsible for educating our immune systems as we grow and for controlling how those immune systems function later in life, as we age. We are just now starting to understand the role our gut microbiome plays in defining our risk of chronic or non-communicable diseases, such as diabetes, arthritis, allergies and cancer.