Dark Matter: The New Science of the Microbiome

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Polyphenols are a naturally occurring antioxidant that helps produce good bacteria in the stomach. It also helps reduce inflammation in the gut. This magic chemical can be found in blueberries and vegetables such as aubergine, tomatoes, white potatoes and peppers. “It occurs in a lot of nightshade vegetables, so we have a lot of that,” he says. A fountain of knowledge and sense in an overwhelming world of science Rhiannon Lambert, Registered Nutritionist and Sunday Times Bestselling Author

Dark Matter by James Kinross - Penguin Books New Zealand Dark Matter by James Kinross - Penguin Books New Zealand

In this mindblowing book, scientist and surgeon James Kinross explains how the organisms that live within us have helped us evolve, shaped our biology and defined the success of our species. But just as we have discovered this delicate and complex ecosystem within us, it is being irrevocably destroyed through antibiotic addition, industrial food production, the globalisation of our diets and lifestyles, and the destruction of our environment. Ray’s response to his FMT treatment was just like that in the reported literature. Within three days of receiving the microbiota transplant he was out of bed. Heather described it as a miracle. If I’ve spent longer than is entirely comfortable talking about faeces, that’s because FMT is a starting point for understanding the importance of the gut microbiome to human health. The extraordinary benefit of FMT in some patients has opened the clinical world to the idea that our microbes may have an important role in the causation and treatment of diseases where their involvement runs contrary to medical science. Tumeric, ginger, and other species are recommended but they’re not a panacea for a healthy gut,” says Dr Kinross. “We have to be quite careful when we’re talking about this. If you’re putting turmeric on fatty sausages, it’s not going to make any difference. Spices have to be part of a bigger nutritional strategy.” Don’t overuse antibiotics As someone with a PhD in Biotechnology, I can confidently say that "Dark Matter: The New Science of the Microbiome" by James Kinross is a fantastic read that I would highly recommend to anyone interested in health and well-being. 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.”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.

Dark Matter review: The amazing story of the microbial world

This is a really nuanced and difficult thing to talk about, because of course, sometimes we have to take medicines,” says Dr Kinross. “I don’t want people to think that if your GP recommends antibiotics you shouldn’t take them.” Ray was readmitted to St Mary’s critically unwell and was soon diagnosed with Clostridium difficile (C diff) infection (officially, this bacteria has now been renamed Clostridiodes). A “hospital-acquired infection”, this disease is a complication of 20th-century medicine and an unintended consequence of Alexander Fleming’s discovery of penicillin, the first effective mass-produced antibiotic, in 1928. It is a global problem that afflicts 500,000 people in the United States each year and it kills 29,000 of them. Eat more omega 3 New research suggests a relationship between gut microbes, omega 3 and brain health Eat fermented foods Tim Spector favours kombucha, kefir and kimchi, as well as unpasteurised cheeses A very small Italian study using a similar commercial probiotic, Sivomixx, piqued his interest after it suggested acute Covid patients treated with it might be less likely to end up in ICU or to die, and eight times less likely to suffer respiratory failure. Bjarnason is hoping to start a larger study in the next few months.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? Some of these studies are extremely encouraging and offer treatments where few effective medical therapies exist. For example, FMT appears to be a promising treatment for irritable bowel syndrome and a recent study suggests that its benefit can last for many years: 125 patients were randomly assigned to receive either 30g or 60g of faeces from the same donor or a placebo transplant containing their own faeces. Researchers not only found that the FMT improved the symptoms, but there was a lasting benefit three years after it was given. 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. Spector’s 30-year-long study of 15,000 twins, TwinsUK, and his PREDICT studies have shown that even genetically identical people respond to the same foods very differently (our microbiomes are so variable that twins share only 30% of the same gut microbes). By feeding participants the same meals on different days, he was able to show that responses to the same meals also vary hugely between individuals, influenced by both the microbiome and genetics. This matters, says the ZOE team, because our response to food is linked to our risk of heart disease, type 2 diabetes and obesity, but also because it blows apart the tired and useless mantra “calories in, calories out”, which doesn’t make sense in a world where two people’s blood glucose levels can be hugely different after eating the same slice of cake. Spector hopes his tests – which don’t just test for microbes, but also assess blood fat and blood glucose responses to specific foods – will change this. “We’re just starting to get to the point where we can suggest individualised foods. This is not just isolated microbiome testing,” he says. “We have trials in place to quantify this, but the initial results are exciting, with nearly everyone reporting weight loss and improved energy levels without any calorie counting or traditional weight loss methods. Previous microbiome tests have been sub-optimal [but the] ZOE approach is completely different: using state of the art sequencing allows us to detect species and strains and find strong associations between these microbes and both foods and health.”

Dark Matter by James Kinross | Goodreads Dark Matter by James Kinross | Goodreads

More than half a century later, the Dutch gastro- enterologist Josbert Keller and his team at the Amsterdam Medical Centre randomised patients with recurrent C diff into three groups. The first group received vancomycin, a wash-out of the colon using a strong laxative, and a faecal transplant. The second had vancomycin and the colonic wash-out, and the third just received vancomycin. The FMT group did so much better than the other two groups that the study had to be stopped early, as it was deemed unethical to continue. In this ground-breaking book, surgeon and expert on the microbiome, James Kinross, takes us on a guided tour of our extraordinary inner universe, showing how our relationship with microbes may hold the key to why we are increasingly succumbing to diseases and conditions such as cancer, Alzheimer's, autoimmune conditions and allergies. He highlights how hyperglobalization and our addiction to antibiotics has transformed our internal ecosystems and why this matters so much to our future health and happiness. If you're a young parent, this book is particularly crucial for you. The gut microbiome plays a significant role in the health of young children, and Kinross provides actionable insights on what can be done to ensure better health for our children in the future. What I particularly loved about this book is its strong scientific foundation. Kinross, a world-leading microbiome scientist and surgeon, offers a wealth of relevant insights drawn from his personal experience and over two decades in the field. The book serves as a much-needed, up-to-date summary of what is going on in this rapidly developing area of study. Dr Ben Mullish, a clinical scientist at Imperial College London, was running a trial of FMT in patients with C diff infections. Ray was so unwell that Dr Mullish offered him the treatment. Heather understood that there are good and bad bugs and advised her husband to go ahead with it, but Ray was not having it. The idea of taking another human’s faeces was just too much for him, and he refused. Three days later, however, he had deteriorated so much that there was no other choice. Ray consented to the trial.But what if I told you that faeces was not toxic waste and that it contained the secret to human health? Would you eat it, if your life depended on it? What if it was rebranded as a faecal microbiota transplant (FMT) or, more accurately, a faecal milkshake given through a tube that passes through the nose into the stomach? You could even take it in the form of a capsule – or “crapsule” – if you wanted. For breakfast, he has high-fibre bran flakes, sometimes supplemented with inulin, a prebiotic fibre. He has that with fruit. “We have overwhelming epidemiological and experimental evidence that says if you can increase your fibre, your risk of heart disease, diabetes, obesity, and cancer, will all go down and you will be healthier.” ‘There are lots of confusing pieces of dietary advice for people as to what to eat,’ says Dr James Kinross (Photo: Westend61/Getty) Do eat fermented food every day

Dark Matter by James Kinross - Penguin Books Australia Dark Matter by James Kinross - Penguin Books Australia

The final frontier for gut microbiome exploration is its relationship with our brains, something the new fields of nutritional psychiatry and psychobiotics are digging into. We already know the gut has its own nervous system, the enteric nervous system, and contains 100m neurons. We also know the gut-brain axis, via the vagus nerve, shoots neurotransmitters produced within the gut around the body and to the brain, which is why Cryan’s lab has studied the impact of particular bacteria on sleep and how certain types of fibre can improve complex cognitive processes.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 eat a lot of fermented foods in our house,” says Dr Kinross, who lives in London with his wife and two children. “We have a lot of kimchi and sourdough. We try to have a meal every day with some form of fermented food. Again, this is the whole microbiome argument. It improves the richness and diversity of the gut. We really like to do that.” Do eat 30 different fruits and vegetables a week The “gut microbiome” is the name we have used to describe not only the wildly diverse collection of microbes that live there, but also what happens when they interact with each other and with our bodies. In other words, it’s an ecosystem made up of trillions of microbial life forms going about their business inside us, as we go about ours. Eat more fibre Most of us eat only half the recommended 30g a day. But start slowly – our guts don’t like rapid change