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You couldn’t live without the microbes in your body.

As Adam Rutherford discovered when he underwent an uncomfortable test, eating probiotic yoghurt may not be enough to maintain a healthy body full of ‘good’ bacteria.

It all started with what can only be described as a brilliant invention. It’s a flattened starfish-shaped fold-out sheet with sticky tabs on the front and back. The tabs are stuck to the toilet seat. When in place, it creates a kind of hammock on which the specimen is displayed, ready for sampling. I put on the rubber gloves in preparation for the procedure.

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I took a sample of the sample with a tiny spoon attached to the inside of a blue lid of a test tube after I had left my deposit on the hammock. I screwed the lid back on tightly to the top of the plastic tube. I wrapped everything in an icepack that I’d frozen earlier. and the valuable cargo was ready for transport.

Map My Gut, the destination, promised to reveal what microbial life lurked inside my bowels. I carried out the experiment for an episode of the BBC radio show The Curious Cases of Rutherford and Fry, which investigated how much of our body’s weight is bacteria. Various findings in recent years have suggested that the microbes in our digestive system are far more important to our health and well-being than previously thought. But I quickly discovered that I was failing miserably at keeping this bacteria alive – and that certain diets can change their fortunes.

Inside our guts, we have around a thousand different species of bacteria. And the total: well, it’s difficult to say how many trillions there are. And almost all of them are doing useful work for us.

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Our genomes have about 20,000 genes, but microbes have 500 times as many. This enables them to perform some pretty amazing tricks, such as aiding digestion, producing vitamins and minerals, and even preventing disease transmission by crowding out and killing infectious bacteria.

But they go beyond that: they have shaped who we are on the inside and outside. “Our microbes help to build our bodies,” Ed Yong, author of I Contain Multitudes, told me. They shape and renew our organs as we age.” They may even have an impact on our behaviour and thinking. Many animal studies have shown that the microbes in their gut can influence their mood, personality, and resilience to anxiety and stress.”

It is unclear how much of these findings will be transferred to humans. But we do know that there is far more variation between people in their microbiomes than in their genomes. Our microbial makeup is influenced by our medical history, location, and diet. Even our closest relatives can have very different signatures.

As a result, I defecated on a paper tray and scooped some out.

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I’ll admit that I was a little nervous when I walked into Tim Spector’s office at St Thomas’ Hospital to receive my results. What would I learn about my bacteria’s mysterious inner world? What could possibly be lurking in my colon?

What were the outcomes? To be honest, it’s pretty bad.

“You are near the bottom of your class. “You’re in the bottom 10% of the population in terms of diversity,” Spector said cheerfully. The kind of delight a scientist feels when he or she discovers something or someone unusual.

He explained that diversity is one of the keys to a healthy gut, with the idea being that different microbes perform different tasks. A diverse workforce brings a wider range of skills to the table.

Diversity is one of the keys to a healthy gut 

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Not only was I lacking in variety, but the bacteria colonies in my gut were less than appetising. My report revealed 65 times the average amount of Clostridium perfringens and 211 times the average amount of E. coli, both of which are associated with gastrointestinal disease.

“These findings suggest you have a very unhealthy microbiome,” my report stated.

I could now use the excuse that I’d just returned from a business trip and had probably eaten something shady. However, Spector believes it would be unusual to shift the balance so far away from a one-time infection.

But what about my beneficial bacteria? Fewer than 100 bacteria species cause infectious disease. Among the thousands of microbes found in our gut are, ‘Mostly harmless,’ as author Douglas Adams would say. So, how did I do against the good guys?

Microbes like Akkermansia and the tongue-tying Christensenellaceae are at the top of the’most desirable’ list. Both are linked to a reduced risk of weight gain. Methanobrevibacter aids in the extraction of more calories from food, allowing you to eat less. Oxalobacter aids in the prevention of kidney stone formation.

How many of these good bacteria did I have? Zero.

Not only was I relegated to the bottom of the class, but my guts had also received a detention. And they couldn’t leave until they took a long, hard look at themselves and decided to change.

So what can I do to improve my microbiome? Variety is the key, apparently, and diversifying your diet helps diversify your bacteria.

People know about live yoghurts, but the next stage up is kefir, a Persian soured milk, which has five times as many microbes  

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Fermented foods are especially beneficial for promoting a healthy microbiome. “People are familiar with live yoghurts, but kefir, a Persian soured milk, has five times as many microbes,” Spector explained. Miso soup and kimchi (pickled cabbage) are also delicious fermented foods for your internal guests.

If all of that sounds a little too rich, garlic, artichokes, bananas, and whole grains are also high in fibre. And the polyphenols in red grapes are one of Akkermansia’s favourite foods. Which I’m using as an excuse to have another glass of red.

Probiotics, which are marketed to help boost our gut bacteria, are rarely worthwhile investments. because there is little evidence that the bacteria in them stick around long enough to change your microbiome. They have, however, been shown to be useful in very young or elderly patients, and can prevent upset stomachs caused by antibiotics. Clearly, it was too late for my bad guts.

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I’ve changed my diet drastically since these shocking revelations. I haven’t eaten meat in over a month as a result of the results. Miso soup has taken the place of meatballs, and kimchi has replaced cod and chips. Despite the fact that the jar of kimchi cabbage smells so bad, my wife insists on keeping it in the shed.

Only time will tell if these changes will have a long-term impact on my microbiome. But I’m aware that I’m no longer eating for myself, but for the trillions of microbes that share my body. Who I’m hoping won’t be imprisoned for too long.