A gut full of diverse microbes – bacteria, viruses and fungi – is essential for a healthy mind and body. And evidence is growing that our modern diet, overuse of antibiotics and obsession with cleanliness are damaging the diversity of microbes that live in our guts, contributing to a range of conditions including depression, multiple sclerosis, obesity and rheumatoid arthritis.

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Microbes live in our guts, bodily fluids, cavities and skin. For every one of our human cells, there’s at least one of them. In an average adult, they weigh in at 1-2kg; similar to our brain. Collectively, they’re called the human microbiota and their genes are the microbiome. Only a few microbes cause disease; most are beneficial and live in peaceful symbiotic coexistence in and on our bodies. We need them and they need us. And if our microbes aren’t healthy, neither are we.

Microbiome and the diet

A healthy microbiome protects against obesity, allergies and diseases as bacteria break down food in the colon, providing energy for themselves and useful byproducts for us. These byproducts are essential components of chemicals that affect mood, appetite, metabolism, inflammation and the immune system. Professor Tim Spector of King’s College London says that variations in the gut microbiome explain, in large part, why our kids are getting fatter and why some individuals gain more weight than others on the same diet. There is no good evidence that we consume more calories or do much less than previous generations, yet people around the world are getting fatter, and Spector says that, while genetics play a part, so does the diversity and types of microbes in the gut.

The gut microbiome is mostly influenced by diet and environment. Babies get their first exposure to bacteria that colonise their guts as they travel down the birth canal. Babies born by caesarean section, as at least a quarter are in the UK, appear to be more prone to obesity. Spector explains that a good diet is a diverse one, with a range of fibre and vegetables including artichokes, leeks, onions and garlic. Polyphenols, found in foods including nuts, seeds, coffee, dark chocolate, red wine, olive oil and berries, are used by microbes as an energy source, with beneficial effects on human immune cells. Foods that nourish the microbiome are called prebiotics, and foods that contain the actual microbes, such as yoghurt and fermented milk called kefir, are called probiotics. Fermented foods, such as sauerkraut, kimchi and miso, are combinations of probiotics and prebiotics, known as synbiotics.

Inflammatory arthritis

An international consortium of scientists is studying faecal samples from people with inflammatory arthritis, such as rheumatoid arthritis. Bacterial groups that seem to be increased can be isolated and introduced to rodents, triggering the development of arthritis in previously healthy animals. Professor Michael Dustin of the University of Oxford says that the risk of developing rheumatoid arthritis is associated with genetic predisposition and environmental factors. “But it’s much easier to modify your microbiota than change your genes,” he says. Tests for rheumatoid arthritis can prove positive several years before symptoms appear, so there’s a window of opportunity to try to stave off the onset of the condition. Using that time to establish a more protective microbiota is one approach being studied. Dustin says that we still don’t know whether dietary changes are enough or whether more radical procedures (such as faecal transplants) are necessary.

Variations in the gut microbiome explain why our kids are getting fatter and why some individuals gain more weight Tim Spector, King’s College London

Diarrhoea

Changes in the gut microbiome can be very dangerous; people treated with prolonged courses of antibiotics that kill a wide spectrum of bacteria can develop life-threatening diarrhoea due to an overgrowth of Clostridium difficile. Faecal transplants (infusions of donor faeces down a nasal tube or up the rectum into the gut) are used to treat these extremely unwell patients, proving that disruption of the gut microbiome can cause serious illness and restoring it to normal can cure the problem.

Multiple sclerosis

About 100,000 people in the UK live with multiple sclerosis (MS), a neurological condition that can cause problems with vision, balance, sensation and movement. Researchers have found specific changes in the microbiome of people with MS that appear to be linked to changes in their immune function. And drug treatment of MS has also been shown to impact on the gut microbiome. Dr David Schley of the MS Society says: “The link between MS and the bacteria living in our intestines is an exciting area of research. Recent studies in mice have indicated that intestinal microbes could influence symptoms. While this early evidence is intriguing, we need to learn more before we can make recommendations over whether people with MS should make changes to their lifestyle or diet.”

Depression

According to the World Health Organisation, depression is the leading cause of disability worldwide. So, there is a lot of interest in the role of the gut microbiome in preventing and treating it. Professor John Cryan of University College Cork says: “We now know that good brain health depends on good gut health. The gut microbiome affects every aspect of brain functioning and human behaviour.” Studies have shown that rats with high levels of bifidobacteria in the gut withstand psychological stress better than those with low levels. And it appears that humans do, too; recent human studies from the Cork group in healthy volunteers show increased brain activity (measured by EEG) and reduced levels of stress (measured by rating scales of anxiety and chemicals in the blood, such as cortisol, that rise in response to stress) when people are given demanding tasks to perform.

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“We know that the more diverse your microbiome, the less likely you are to be frail or have cognitive impairment. And a diverse diet is what drives a diverse microbiome,” says Cryan. Microbes from the guts of depressed people have been fed to healthy rats, which then develop depression and anxiety-like behaviours. Other healthy rats, fed microbes from the guts of people without depression, remain well.

“It’s an exciting area but we need to find out just how gut bacteria send signals to the brain,” says Cryan. “There’s no downside to recommending a diverse Mediterranean-style diet that includes lots of fibre and cuts down on emulsifiers, processed foods and artificial sweeteners.” Probiotics sold commercially are largely unregulated, are of unknown effectiveness and may not reach the colon alive. “We can’t even be sure a lot of them get past the stomach acid,” he says. But Cryan thinks that within the next five years we will learn a lot more about which specific bacteria are important and we will be able to test our personal microbiota and supplement deficiencies. “It’ll become like getting your cholesterol checked,” he predicts.