Dark Matter: The New Science of the Microbiome

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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.

Dark Matter: The New Science of the Microbiome : Kinross Dark Matter: The New Science of the Microbiome : Kinross

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? Instead, Dr Kinross recommends: “I would sit down with my doctor and ask, what medicines am I taking that I don’t really need to be on? You might be taking proton pump inhibitor medicines for changing the acidity of the gut, or any kind of unnecessary painkillers. Do I really need to be on medicines to control my blood lipid chemistry or are there things that I could change in my lifestyle that would reduce my blood cholesterol?”A spellbinding explanation of microbiology that will help you get to the bottom of health and happiness John Vincent, Co-Founder of Leon

Ready for your crapsule? Faecal transplants could play a huge

Kinross specialises in the detection of colon cancer and benign conditions of the gut. In his 18-year career, he has researched gut microbiome extensively and is the author of Dark Matter: The New Science of the Microbiome. He has learned that “lifestyle is overwhelmingly important for the gut”. The sense of revulsion we feel when we’re faced with human excrement (or even just the thought of it) is, in part, a response to the way it looks and smells. But that revulsion is also a psychological reflex, ingrained by potty training and social stigma. This aversion is an important safety mechanism: handwashing and sewer systems prevent the spread of diseases that have killed millions. 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 Dr Kinross advises eating around 30g of fibre a day. “Fibre is broken down by bugs in your gut. We don’t metabolise fibre, the bugs do that on our behalf. This helps grow those molecular goodies, that promote health. Fibre also absorbs toxins in the gut.”

Two Christmas trees? We’ll be having at least five in our house

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 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. 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. Eat fermented foods Tim Spector favours kombucha, kefir and kimchi, as well as unpasteurised cheeses Engaging ... [ Dark Matter] stands out in revealing the microbiome through the eyes of a clinician who sees each patient not just as a human, but as a human entwined with a complex, dynamic ecosystem New Scientist

Dark Matter By James Kinross | Used | 9780241543979 | World Dark Matter By James Kinross | Used | 9780241543979 | World

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.” Eat more fibre Most of us eat only half the recommended 30g a day. But start slowly – our guts don’t like rapid change 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. 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.The scale of the task is huge: there is 1.5kg of bacteria in our guts.’ Illustration: Lisa Sheehan/The Observer Everything 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.” 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. Eat more omega 3 New research suggests a relationship between gut microbes, omega 3 and brain 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.”

Good Sh*t

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. 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.” If you want to learn more about what’s going on in your gut, the first step is to turn your poo blue. How long it takes for a muffin dyed with blue food colouring to pass through your system is a measure of your gut health: the median is 28.7 hours; longer transit times suggest your gut isn’t as healthy as it could be. We are only now beginning to understand the importance of the gut microbiome: could this be the start of a golden age for gut-health science? While an FMT might be a new idea to many of us today, the medical practice of faecal transplant is ancient, and it has been drunk as “yellow soup” since the 4th century AD for the treatment of infective diarrhoea. In 1958 an innovative surgeon, Dr Ben Eiseman, administered faecal enemas to his patients in Denver, Colorado, with severe and recurrent C diff infections. It was remarkably effective, but like all important medical discoveries, this intervention was largely ignored at the time of its first report.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.