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How to revitalise your gut and stop killing off microbes

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If a diverse range of the right microbes in our gut is the key to good health, what’s the best way to encourage them? We can start by not accidentally killing them off, the experts say.

Wouldn’t it be convenient if there were one thing behind the rise of so many of the health issues plaguing us in the 21st century, such as obesity, type 2 diabetes, allergies and intolerances, irritable bowels, depressed and anxious minds.

All these things are being linked by emerging science to the microbes in our gut, that community of 30-40 trillion microscopic creatures that interact with our body systems in complex and still largely mysterious ways. Since the middle of last century, we’ve been slaughtering them with antibiotics and starving them with our diets, and now we’re paying the price. Or so the argument goes.

RelatedArticlesModule - Gut health microbes Michael Mosley

This is a fast-evolving area of science and much is still not known. That’s never stopped British doctor-turned-broadcaster Michael Mosley from using his influence to convince the masses to alter their lifestyle in response to the latest research.

There have been books, TV shows and websites preaching the benefits of intermittent fasting (he developed the 5:2 diet) and the effectiveness of very-low-calorie regimes at reversing diabetes. Now, Mosley has the microbiome in his sights with a new book, The Clever Guts Diet, and its accompanying The Clever Guts Diet Recipe Book.

Gut guru Michael Mosley is coming to Auckland to speak about his new book on January 21, 2019, tickets are available here.

What’s going on in there?

Microbial restoration is one of medicine’s new frontiers. Already we’re treating severe intestinal infections using faecal transplants from healthy donors. At Auckland’s Liggins Institute, there’s a groundbreaking study under way, dubbed the Gut Bugs Trial, in which bacteria from healthy, lean young people are being given in capsule form to teenagers who are clinically obese (this kind of thing has led to dramatic weight loss in mice).

Michael Mosley.

As ever, Mosley’s is more of an everyday, do-try-this-at-home approach. He’s among those who believe it’s possible to help the microbiome to bounce back with a diet based around foods that are good for it.

Until relatively recently, it was impossible to study the thousands of different species living in our gut because most don’t survive when removed from our intestines. But in the wake of the Human Genome Project, scientists are now able to sequence the DNA of the microbes expelled in our stools. It’s still tricky, however, for most of us to find out exactly what’s going on – and potentially wrong – in there.

Online you’ll find several companies offering to sequence your microbiome. Mosley sent a poo sample to one called uBiome and was gratified to learn he has a lower-than-average population of Firmicutes, which have been linked with obesity, and lots of Bacteroidetes and Akkermansia, which are associated with leaner body types and less inflammation in the gut.

“But it’s not at all clear how reliable this is,” he concedes. “If I sent off my poo sample to five different centres, I don’t know whether I’d get five different results. I suspect there’s a lot of variability.”

This lack of clear-cut diagnostic testing is one of the reasons sufferers of disorders such as irritable bowel syndrome and leaky gut have had to put up with a fair amount of eye rolling from their doctors.

“We’re all quite simple as doctors,” says Mosley’s wife, Clare Bailey, who as well creating The Clever Guts Diet Recipe Book is also a practising GP. “We like to measure, define and test things, otherwise we feel a little bit awash. And this is an area where the science isn’t that clear yet. You can make a guess at how wrecked people’s microbiomes are by asking about their diet, how they’re feeling and what their symptoms are, but it’s not something that’s routinely picked up.”

Even the autoimmune disorder coeliac disease, characterised by a severe reaction to gluten, is under-diagnosed partly because the test commonly used to pick it up involves detecting antibodies produced in response to gluten, and most sufferers have been experiencing such unpleasant symptoms they’ve stopped eating foods containing it long before they turn up to be tested.

Obesity is another area in which doctors are struggling. Bailey says she’s spent years advising her patients to eat less and do more exercise, but in most cases it’s been futile. Thanks to research by microbiologists, we now have a possible reason. It turns out that overweight people have a higher proportion of Firmicutes, a group of bacteria that are good at extracting extra calories from the food they consume. When the gut microbes of obese mice are transferred into specially raised germ-free mice, they get fatter – hence the Gut Bugs Trial at the Liggins Institute, which aims to do the opposite.

Husband and wife Clare Bailey and Michael Mosley.

Call in the troops

What we know for sure is that the community of bacteria in the gut is in a constant state of flux, as our microbes compete for space and resources. “It’s a pretty ferocious war,” says Mosley. “You have survival of the fittest going on down there, although you may not be aware of it. They’re all fighting for dominance. So, yes, it’s war and we need to parachute in reinforcements every so often.”

Unfortunately, the modern lifestyle has unbalanced this battle. Broad-spectrum antibiotics, which wipe out friendly bacteria along with life-threatening infections, are only partly responsible. The typical Western diet also needs to be held accountable, which means another black mark against highly processed foods.

“Emulsifiers, which are a form of detergent, are added to them for texture and to extend shelf life,” says Mosley. “Feeding common emulsifiers to mice tilts their biome in an unhealthy direction and encourages the growth of bacteria that attack the mucous lining of the gut.”

The equilibrium of microbes also appears to be affected by a diet high in sugar and fat. One Italian study comparing the gut microbiota of children in Florence with those living in a rural village in Africa’s Burkina Faso (where they exist mostly on a savoury porridge of millet and sorghum, vegetables and the odd chicken), found the Italian kids mainly had microbes belonging to the Firmicute group, whereas the Burkinabés’  were dominated by Bacteroidetes.

There are plenty of other factors. In the West, drinking-water supplies are often chlorinated and fluoridated. Cheeses are pasteurised. Our lives are increasingly sterilised and sedentary. “We don’t go out as much, we live in more atmospherically controlled circumstances, our kids don’t run around in the dirt like they used to,” says Mosley.

All of which has been unhelpful to a group of beneficial microbes known as the Old Friends, which evolved with us and are essential for a properly functioning immune system. Their gradual demise is being linked to the rise in allergies and autoimmune disorders.

A study found high gut levels of lean-making Bacteroidetes in Burkina Faso kids. Photo/Getty Images

What to eat

The future may involve personalised diets and prescribed supplements that parachute in reinforcements of whichever friendly bacteria people need to treat their specific conditions and then ensure the environment is right for them to flourish. Since we’re not quite there yet, taking an over-the-counter probiotic supplement may seem the best option. Selling them is certainly a burgeoning business, but there’s some doubt about the effectiveness of many products on the market. The problem is our gut hosts thousands of different strains and species of bacteria, yet over-the-counter supplements and yogurt drinks tend to contain a relatively small number of the same strain, which, if they do reach the gut, might not survive the battle raging there.

Mosley is all for people taking a good-quality multi-strain product for extra support when on antibiotics (some have been shown to prevent diarrhoea), but in general he’s not a fan of relying on supplements.

“If you have allergies like hay fever, it’s unlikely you’ll need the same strains of bacteria as if you have irritable bowel syndrome,” he says. “I’m not dismissing probiotics, I’m just cynical about some of the products that are out there at the moment, and if you’re going to buy one, you want to know it has some science behind it. On the other hand, I think probiotics in the form of food are terrific. Fermented foods, smelly French cheeses, live yogurt – all the things that have an abundance of the stuff, great.”

It seems that the clearest marker of an unhealthy gut is losing species diversity and that therefore the wider variety of healthy foods you can include in your diet, the better. “You may think you’re getting a huge variety,” says Mosley. “You go into your supermarket and see this huge range of foods, but most of them contain relatively few ingredients: wheat, sugar, homogenised fat.”

We undoubtedly need to cut down on sugar, which is toxic to bacteria in large amounts, and give artificial sweeteners a swerve, as they’ve been shown to have a deleterious effect on the gut microbes of mice. Instead, we should be exploring the world of fermented foods, such as sauerkraut, kimchi and kefir.

There have been concerns that lots of the “good” bacteria in the foods don’t survive the acidic environment of the stomach. “But the great thing about fermented foods is that the microbes growing in them have been selected to be massively resistant to acid attack and the evidence is strong they do get through,” says Mosley, who did a small experiment for his TV show Trust Me, I’m a Doctor that followed groups of people consuming either a popular sugary probiotic yogurt drink or fermented milk drink kefir and found measurable changes in the stools of those who’d been drinking kefir.

Once the microbes are in there, you have to feed them. Fibre in almost any form is helpful, but what good bacteria really need is prebiotics, plant fibres the body can’t digest, which act a bit like fertiliser. One of the best known is inulin, found in common foods such as onions, leeks, garlic, asparagus and bananas, particularly green ones.

Fun fact: if you cook then cool potatoes, pasta, peas, beans and lentils, you significantly increase the amount of prebiotic-resistant starch in them. Since it evades digestion, this resistant starch reaches the colon largely intact, meaning it shouldn’t create blood-sugar spikes. Once the helpful bacteria have digested it, they produce a short-chain fatty acid called butyrate that reduces inflammation and strengthens the gut wall.

Italian children had mostly fat-linked Firmicutes. Photo/Getty Images

Completing the puzzle

Mosley admits to not being the most adventurous eater. In his youth, he avoided vegetables and ate what he describes as a mostly beige diet punctuated by the odd slice of bright-pink salami. These days, his meals are focused on foods his microbes like.

He’s trying especially hard to enjoy edible seaweeds because they’re an excellent prebiotic. Feeding them to sows has been shown to have effects on their piglets, which, when hosting fewer nasty bacteria such as E coli in their gut, require fewer antibiotics. Research at Australia’s University of Wollongong found people who took seaweed capsules boosted the population of gut bacteria that produce butyrate; there was an accompanying reduction in inflammation and an increase in insulin sensitivity – so good news all round. In fact, that study was extended to see how this decrease in inflammation might affect people with hard-to-treat psoriatic skin disorders.

“I’m still trying to acquire a taste for seaweed,” admits Mosley. “Clare keeps slipping it into our meals. I’m struggling slightly with it but I recognise the benefits.”

At least he still gets to enjoy a glass of red wine and a couple of squares of dark chocolate, since the polyphenols they contain appear to influence the microbiome, increasing Bifidobacteria, which are associated with lowering cholesterol.

Watch Mosley explain how you can lose 14 kilos in 8 weeks with his refined intermittent fasting diet, The Fast 800:

There may still be significant gaps in the science but Mosley is encouraged that so many of the foods associated with a healthy gut colony are those eaten in the world’s Blue Zones, the areas where people live longer, healthier lives. He’s also heartened to find so much of the latest research fits neatly with his previous work promoting the benefits of a Mediterranean-style diet and intermittent fasting.

“I’m thrilled that the science is all going in my direction. I was really delighted to discover that when you’re doing intermittent fasting and reducing your calories, it increases the growth of a bacterium called Akkermansia that lives in the mucus that forms on the gut wall. It thrives when its rivals aren’t being fed, so it tends to proliferate when you’ve been starving. It’s very involved with producing butyrate and strongly associated with leanness, strengthening the gut wall and reducing inflammation.”

Inflammation is another area of medicine that’s hot. “We’re increasingly realising it’s critical to obesity, diabetes, dementia, heart disease – you name it. And it seems a lot of these things may actually begin in the gut,” says Mosley.

He’s in touch with researchers around the world, following their trials and seeing the results before publication. Meanwhile, his wife is putting what he learns into practice with her patients.

“She actually changes people’s lives directly and we get an enormous amount of feedback – they send emails and stop me on the street,” he says.

Genetic epidemiologist Tim Spector. Photo/Alamy

“Re-wilding” the gut

Although the Clever Guts Diet wasn’t designed specifically for weight loss, people have contacted Mosley to say this shift to a healthier way of eating has resulted in them dropping kilos. He’s aware he wouldn’t be in the greatest shape himself if he’d stuck with his “beige” diet.

A couple of years ago, he did an experiment in which he lived on mostly processed foods for four weeks, including lots of bacon, sausages and salami. He gained 3kg, mostly around his belly; his blood pressure went up; and the diversity score of his gut bacteria fell.

He was repeating a similar, headline-grabbing trial performed by London professor of genetic epidemiology Tim Spector, who talked his son Tom, a genetics student, into eating nothing but food from the local McDonald’s for 10 days. By the end, Tom had lost an estimated 1400 species of gut bacteria – nearly 40% of his total.

Spector believes we all need to “re-wild” our gut bacteria, having seen a huge improvement in the diversity of his own microbiome after spending time living and eating with an African hunter-gatherer tribe. He leads the crowdfunded British Gut Project, a large-scale collection of samples looking at the bacterial communities of the mouth, skin and vagina, as well as the gut, that aims to provide information about how diet and lifestyle influence the microbiome and how we can change it to improve our health.

Spector has researched the impact different microbes have on twins and, like Mosley, advocates avoiding junk food and enjoying a diverse diet with lots of fibre, fresh and fermented foods, and occasional short periods of fasting.

How much you exercise also influences the microbiome. There’s growing evidence that an active lifestyle enriches microflora diversity and improves the Bacteroidetes/Firmicutes ratio, which may contribute to weight loss.

If you’re a woman of childbearing age, there’s extra incentive to pay attention to all this because you’ll be passing on some of your bacteria population to your baby. Babies get a dose during birth as they pass through the vagina and past the anus (a reason for concern about the increase in Caesarean-section births), then compounds in breast milk help those useful microbes proliferate.

With theories about the role the microbiome may be playing in the rise of anxiety, depression and perhaps even autism, Mosley is excited about the potential all this new science has to improve the health of vast numbers of people with minimal medical intervention.

“Once upon a time, we were all obsessed by the genome, and that’s still very exciting, but the reality is you can’t change your genes,” he says. “However, in a relatively rapid period of time, you can change your biome and that’s what makes it more applicable to normal human beings.”

The Clever Guts Diet, by Michael Mosley (Simon & Schuster, $35).

This article was first published in the November 25, 2017 issue of the New Zealand Listener.