Secrets of the gut doctor: From faecal transplants to microbiome testing - the new treatments that could transform your entire health

Have you ever considered the trillions of teeming bacteria which are spinning around your gut right now, breaking down breakfast into human compost?

Well, prepare to get up close and personal. Thanks to a new era in affordable testing, anyone can have their personal colonies of bacteria – called the microbiome – tested and the results analysed to show just what the little critters are getting up to. If anything.

And the fascination with our insides doesn’t stop there – a new generation of gut specialists are offering ways to tune up our microbiomes via therapies from oral supplements to (steel yourself) human poo transplants.

This new interest in our interior nitty gritty is a natural progression from the idea that we are all stuffed full of “good” bacteria and “bad” bacteria – and that if you don’t have enough of the former, the latter will triumph in some kind of guerrilla war which leads ineluctably towards an upset stomach.

But now science is suggesting our microbiome affects far more than just digestion. Researchers worldwide are speculating it could play a role in everything from our mental health, to our obesity and fertility levels, as well as our ability to combat diseases ranging from cancer to Parkinson’s, plus more obvious gut-related conditions such as Crohn’s disease. A new Swiss study in has even suggested that microbiota can affect how well we metabolise pharmaceutical drugs, too.

However, there’s plenty that is still mysterious – how the bacteria affect so many different conditions, how they work together, how they can get out of balance and how that balance can be restored.

Perhaps it’s no surprise, then, that home microbiome testing is becoming popular, especially as all it takes is a quick stool sample and a little patience: results take about two months to come back.

With that in mind, I recently put my own flora under the microscope, using an AtlasBiomed test offered by Welsh kefir producers Chuckling Goat, which results in a 70-odd page report for £129.

The results are detailed and well explained, with your bacteria counts and related chances of certain diseases marked out of 10.

The first – and probably least disputed category – is diversity. Although so much of the microbiome is a mystery, what is uncontested is the need for variety. Your gut should be like a sort of bacterial , as we need lots of different bugs – working together and alone – to reap the benefits.

Mine, however, was depressingly vanilla. Out of 10, I scored 4 for diversity – of the strains I did have, I only scored 4 out of 10 for quality, too. In particular, I had almost no – normally one of the most common and beneficial bacteria in the human gut, which helps to keep “bad” bacteria levels in check

Worst of all, the report said that my microbiome isn’t even British, it is ‘North American’. Which is to say, that it is most commonly found in those who often eat sweets, fizzy drinks, fried and fast food. So frustrating – as I follow a mostly Mediterranean diet of fresh veg, fish and olive oil, honestly.

Shann Jones, co-director of Chuckling Goat, explained to me that my results weren’t alarming; just signs of a system out of balance, which needed support.

“Think of your microbiome as the Amazon rain forest,” she says. “When it’s healthy, it contains lots of different species. But if it gets polluted, some wildlife dies off and can’t replace itself. In our microbiomes this can be due to antibiotics, illness or diet. So, it’s not ideal but it can be improved.”

Dr Julian Kenyon of the Dove Integrated Medical Care centre in Twyford, Hampshire has also had his microbiome tested. His results were good, he says, although his overall profile matched that of ‘Worldwide Peasants’ – the opposite to mine, suggesting a diet rich in vegetables, seeds, and grains.

“That’s not so surprising,” he says. “I have a very varied diet, which is also true of people across the world who don’t rely on processed food or refrigeration.”

Dr Kenyon has long had an interest in the gut – an early UK pioneer in probiotic supplements (which aim to replace levels of good bacteria), many of his patients come for intractable conditions such as chronic fatigue syndrome (CFS) and irritable bowel syndrome (IBS), so offering microbiome testing has been a natural step.

However, not everyone is convinced of the usefulness of testing. Registered Dietitian Samantha Gill, a spokesperson for the British Dietetic Association, says: “We don’t know what the ‘optimal’ or ‘perfect’ microbiome looks like. Our microbiome differs from person to person and along the gut.

“Microbiome testing is still in its infancy and overall, the information provided will generally be limited, because our understanding of the microbiome is still evolving. Also, different companies use different methods, so you’re likely to get a different result.”

She adds: “Testing your microbiome only provides a ‘snapshot’ of that particular point in time. If we were to have another test the day or week after, there is a good chance the results would differ.”

Ben Mullish, clinical research fellow in gastroenterology at Imperial College London, agrees that we can’t read too much into microbiome testing yet, even though it is clearly of use.

“We know that certain gut bacteria are associated with certain conditions,” he says. “The difficulty is we don’t know if these changes in bacteria are a cause of the condition, or consequence of having it. We don’t know if it is down to bad diet or the result of medication for example.”

And he adds: “It’s not just about what bugs are there, but what are their functions, how do they interact? Read-outs give you composition data but don’t say what bacteria is doing. As it stands, with the current amount of knowledge we have, stool microbiome testing shouldn’t be used to influence clinical decision making.”

Regardless, what scientists know is that some unhappy microbiomes respond to faecal microbiota transplants (FMT) – in layman’s terms, poo transplants, from fit, healthy donors such as young sportsmen, which help to repopulate your gut with the ‘good’ stuff.

The process itself is less gruesome than it sounds – transplants can be administered via a pill, a naso-gastric tube or into the colon via a slender catheter (a sort of enema in reverse).

So far, scientific trials have shown that a single treatment of FMT has an 80-90 per cent chance of curing infection with the superbug Clostridium difficile (C. diff). Other studies, says Mullish, are looking into its use for liver conditions, IBS and ulcerative colitis, though there is yet to be conclusive evidence.

“Experience with FMT overall is that it is generally safe when administered in a hospital setting,” he adds. Yet is not without concerns. In the US, a clinical trial into FMT has just been halted after the death of a patient when the sample he was given was found to contain a strain of multi-drug resistant E. coli. Another patient in the same trial has fallen ill – although both were already immuno-compromised before they underwent treatment.

FMT is carefully regulated in the UK, however, with strict guidelines about who should or should not have it. Donors are regularly screened to exclude people recently in areas with traveller’s diarrhoea, a family history of gut disease, or serious diseases. Transplants are on offer privately, if still considered unconventional by many in the field, who dispute their benefits.

Dr Kenyon has tried one himself, claiming results over the following three months which surprised him. “I lost one and half stone without dieting, my hair grew thicker and my sleep improved. There was a definite improvement in my memory and sense of cognition, too.”

He adds: “I wasn’t actually ill, but I got benefits which I hadn’t expected, with no downside.”

At Dr Kenyon’s clinic, 10 sessions of FMT cost around £4,000. He has already published one small study in the , which suggests that faecal microbiome testing is “clinically useful”, and says he has seen “significant success with infertility and failed IVF” after treating patients’ microbiomes with FMT.

A new study, which is pre-publication, reports that “FMT is a safe and a promising treatment for Chronic Fatigue Syndrome associated with IBS”.

Promising as it may be, Gill says we should concentrate on cultivating our own gut flora before considering adding someone else’s. Not fancying FMT myself, I’m relieved to hear that adjusting my diet might be enough to sort out my microbiome.

“Fill up on fibre,” Gill suggests. “Fruit, veg, nuts, seeds, wholegrains, legumes. Some (such as artichokes, onion, garlic) contain natural prebiotics which are ‘food’ for our gut microbes.” She recommends yoghurts and fermented foods, which includes sauerkraut and kimchi, as they contain probiotics which will help to recolonise levels of good bacteria.

Gill points out that some evidence suggests that sweeteners and smoking can both negatively affect the microbiome. And that you could see results quickly. “There are studies showing that significant shifts in dietary intake can alter our gut microbiota within a few days. Our microbiome is ‘flexible’– it will change depending on what you feed it.”

Shann Jones (naturally) recommends drinking fermented kefir made from goat’s milk as it contains many strains of live bacteria: “You are the steward of your own ecosystem,” she says, “love it, feed it, don’t poison it.”