The Gut Doctor
How to beat fatigue, obesity and IBS
‘We still don’t know what the perfect bacteria mixture looks like’
‘It’s not just about what bugs are in your gut, but about how they interact’
Have you ever considered the trillions of bacteria 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 teeming colonies of bacteria – called the microbiome – tested and the results analysed to show just what the little critters are getting up to. If anything.
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) transplants of human faeces.
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 a kind of guerrilla war that leads ineluctably towards an upset stomach.
Now, however, science is suggesting that our microbiome affects far more than just digestion. Researchers worldwide are speculating that it could play a role in everything from our mental health to obesity and fertility levels, our ability to combat diseases ranging from cancer to Parkinson’s, as well as more obvious gut-related conditions such as Crohn’s disease. A new Swiss study, published in the journal Nature, has even suggested that microbiota can affect how well we metabolise pharmaceutical drugs. However, there’s plenty that is still mysterious: how the bacteria affect so many medical conditions, how they work together, how they can become 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 are returned after about two months.
With that in mind, I recently put my own flora under the microscope, using an Atlas Biomed test offered by Chuckling Goat, the Welsh kefir producer, 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 agreed on is the need for variety. Your gut should be like a sort of bacterial Britain’s Got Talent, as we need lots of different bugs – working together and alone – to reap the benefits. Mine, however, was depressingly vanilla: I scored four out of 10 for diversity, and the strains I did have scored four out of 10 for quality. In particular, I had almost no Bifidobacterium – normally one of the most common and beneficial types of bacteria in the human gut, which helps to keep “bad” bacteria levels in check. Worst of all, the report said my microbiome wasn’t even British, but “North American”; which is to say that it is most commonly found in those who often eat sweets, fizzy drinks, fried and fast food – a frustrating outcome, as I follow a mostly Mediterranean diet of fresh veg, fish and olive oil. Honestly.
Shann Jones, the co-director of Chuckling Goat, explained that my results weren’t alarming, but a sign of a system out of balance that needed support. “Think of your microbiome as the Amazon rainforest,” 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 Clinic for Integrated Medicine in Twyford, Hampshire, has also had his microbiome tested. His results were good, he says, with an overall profile matching 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. He was an early UK pioneer oneer in probiotic supplements (which aim to replace levels of good bacteria), and many y of his patients have intractable conditions itions such as chronic fatigue syndrome ome (CFS) and irritable bowel syndrome ome (IBS), so offering microbiome testing sting has been a natural step. However, not everyone one is convinced of the usefulness of testing. ting. Samantha Gill, a registered gistered dietitian and spokesman an for the British Dietetic Associ- ssociation, says: “We don’t on’t know what the ‘optimal’ mal’ or ‘perfect’ micro- robiome looks like. Our ur microbiome differs rs from person to person and along g 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, a clinical research fellow in gastroenterology at Imperial College London, agrees that we should not read too much into microbiome testing, 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 a consequence of having it. We don’t know if it is down to bad diet or the result of medication, for example.”
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 a type of 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 do 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 nasogastric 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 to
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, although 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 drug-resistant E. coli. Another patient in the same trial has fallen ill, although both were already immunocompromised before they underwent treatment.
FMT is carefully regulated in the UK, however, with strict guidelines about who should have it. Donors are regularly screened to exclude people with a family history of gut disease or serious conditions, or who have recently visited areas affected by traveller’s diarrhoea. Transplants are on offer privately, but are considered unconventional by many in the field, who dispute their benefits.
Dr Kenyon has tried one himself, claiming that the results over the following three months surprised him. “I lost one-and-a-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 Hu
man Microbiome Journal, 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 study yet to be published 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, whole grains, legumes. Some (such as artichokes, onion and garlic) contain natural prebiotics which are ‘food’ for our gut microbes.” She recommends yogurts and fermented foods such as sauerkraut and kimchi, as they contain probiotics that will help to recolonise levels of good bacteria.
Gill points out that some evidence suggests that sweeteners and smoking can 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.”
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.”