For a healthy body full of ‘good’ bacteria, you may need to do a lot more than eat a probiotic yoghurt, as Adam Rutherford discovered when he took a rather uncomfortable test.

It began with what can only be described as an ingenious invention. It’s a fold-out sheet, with sticky tabs at the front and back, like a flattened starfish. The tabs stick to the loo seat. When in place, it forms a kind of hammock onto which the specimen is presented, ready for sampling. I slipped on the rubber gloves to prepare for the procedure.

Once I had left my deposit on the hammock, I took a sample of the sample, with a tiny spoon, fixed to the inside of a blue lid of a test tube. I screwed the lid tightly back on to the top of the plastic tube. I wrapped it all in an icepack I’d frozen earlier, and the precious cargo was ready for dispatch.

The destination – Map My Gut – promised to reveal what microbial life is lurking inside my bowels. I conducted the test for an episode of the BBC radio series The Curious Cases of Rutherford and Fry, exploring how much of our body’s weight is bacteria. In recent years, various findings have suggested that the microbes in our digestive system are far more important to our health and well-being than originally thought. But I’d soon discover that I was failing badly at keeping this bacteria thriving – and that certain diets can transform their fortunes.

Methanobrevibacter helps squeeze more calories out of food

We contain, on average, around one thousand different species of bacteria inside our guts. And in total: well, it’s difficult to count, but there are trillions. And they are almost all doing useful work for us.

Our genomes contain around 20,000 genes, but our microbes carry around 500 times more. This allows them to perform some pretty awesome tricks – they help digest food, produce vitamins and minerals and even stop us from catching diseases by crowding out and killing infectious bacteria.

But they go even further than that: they have shaped who we are on the inside and out. As Ed Yong, author of I Contain Multitudes told me, “Our microbes help to build our bodies, they sculpt and renew our organs as we get older.

“Perhaps they may even influence our behaviour and the way we think. There have been lots of studies in animals showing that the microbes in their gut can influence their mood, personality and resilience to anxiety and stress.”

How much these results will carry over into humans is yet to be understood. But what we do know is that there’s a much bigger variation between people in our microbiome than there is in our genome. Our microbial makeup depends on our medical history, our location and our diet. It’s a signature that can be very different to even our closest relatives.

There are better foods than yoghurt for boosting good bacteria

So that’s why I defecated on a paper tray, and scooped a bit out.

I’ll admit to being a bit nervous walking into the office of Tim Spector, a professor of genetics at St Thomas’ Hospital, to receive my results. What would I discover about the mysterious inner world of my bacteria? What exactly would be lurking in my colon?

And the results? To be honest, pretty crap.

“You are near bottom of the class. You’re in the lowest 10% of the population for diversity,” Spector told me, with just a hint of joy in his voice. The kind of joy a scientist has when they discover something, or someone, who is a bit unusual.

Diversity is one of the keys to a healthy gut, he explained, the idea being that different microbes perform different tasks, and a diverse workforce brings more skills to the table.

Diversity is one of the keys to a healthy gut  

Not only was I lacking in variety, but the gangs of bacteria that were hanging out in my guts were less than savoury. My report revealed 65 times more Clostridium perfringens than average, and 211 times more E. coli – both associated with gastrointestinal disease.

“These results indicate you have a very unhealthy microbiome,” stated my report.

Now, I could make the excuse that I’d just been on a work trip and had probably eaten something dodgy. But according to Spector it would be unusual to tip the balance quite that far from a one-off infection.

But what about my good bacteria? Fewer than 100 species of bacteria cause infectious disease. The thousands of types of microbes found in our gut are, as the author Douglas Adams would say, ‘mostly harmless’. So how did I fare on the good guys?

Top of the ‘most desirable’ list are microbes like Akkermansia and the tongue-tying Christensenellaceae. Both are associated with protection against weight gain. Methanobrevibacter helps squeeze more calories out of food, meaning you can eat less. Oxalobacter helps to prevent the formation of kidney stones. 

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

Not only was I dumped at the bottom of the class – my guts had been served a detention. And they weren’t allowed out until they took a long hard look at their behaviour and decided to change.

Clostridium perfringens is associated with gastrointestinal disease

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  

Fermented foods are especially good for encouraging a healthy microbiome. “People know about live yoghurts, but the next stage up which has five times as many microbes is kefir, a Persian soured milk,” Spector told me. Other fermented foods like miso soup and kimchi (pickled cabbage) are a delicious feast for your internal lodgers.

If that all sounds a bit rich, then garlic, artichokes, bananas and whole grains are also good fibrous fodder. And the polyphenols in red grapes are one of the favourite meals of Akkermansia. Which I’m taking as a good excuse for another glass of red.

Probiotics, marketed to help boost our gut bacteria, are rarely worth investing in, as there’s little evidence the bacteria in them stick around to change your microbiome in the long term. They have been shown, however, to be useful in very young or old patients, and can prevent upset stomachs from taking antibiotics. Too late for my bad guts, clearly.

Since these shocking revelations, I’ve had a total diet makeover. It’s been over a month now after the results, and I haven’t eaten meat since. Miso soup has replaced meatballs, and kimchi is the new cod and chips. Although the jar of kimchi cabbage smells so funky, my wife makes me keep it in the shed.

Only time will tell if I these changes will permanently alter my microbiome. But I know that now I am not just eating for me, but for the trillions of microbes that share my body. Who I am hoping won’t be dumped in detention for too long.​