The Master Regulator

Inside you, right now, lives a community of around 38 trillion bacteria, roughly as many as the cells that make up your own body.¹ Most of them live in your gut. For a long time they were seen as passengers. Today, scientists are discovering that they may be closer to the conductors of the whole orchestra.

A hidden organ

Together, these microbes and their genes are known as the microbiome. Between them, they carry more than 3 million genes, over 150 times the number in the human genome.² That gives them a vast toolkit for making substances our own bodies can't. (See Not Written in Stone.)

They break down fibre we can't digest, make vitamins such as vitamin K and some B vitamins, and produce hundreds of compounds that travel through the bloodstream to almost every part of the body. Some scientists now describe the microbiome as a "forgotten organ".

The guardians of immunity

Much of your immune system lives in and around your gut, where it meets the outside world in every meal. Here, your microbes act as teachers, helping immune cells learn the difference between friend and foe.

When gut bacteria ferment fibre, they make short-chain fatty acids such as butyrate. Butyrate feeds the cells lining your gut, helps keep that lining strong, and encourages the growth of special immune cells that calm inflammation.³ In other words, the fibre on your plate becomes, with your microbes' help, one of your body's own anti-inflammatories. (See The Quiet Fire.)

When the balance is lost

When the community of microbes in the gut falls out of balance, with too little variety, too few of the helpful species or an overgrowth of less friendly ones, it's known as gut dysbiosis. It is one of the most common imbalances naturopaths address in clinic, and it can show up in many ways: bloating, wind, irregular bowels, tiredness, food sensitivities, skin flare-ups and low mood. (See Where Body Care Meets Mind.)

A healthy microbiome also helps keep the gut lining strong and tightly sealed. When that lining is weakened, sometimes called "leaky gut", more of the gut's contents can come into contact with the immune system, which may help fuel inflammation elsewhere in the body. This is an active and fast-growing area of research.

Because the gut and the immune system are so closely linked, scientists have found differences in the microbiome in a wide range of conditions:

• Digestive conditions, including irritable bowel syndrome (IBS) and inflammatory bowel diseases such as Crohn's disease and ulcerative colitis. People with Crohn's often have fewer of Faecalibacterium prausnitzii, a bacterium that helps calm inflammation.⁴
• Allergies, eczema and asthma. In a Canadian study, babies with lower levels of four types of gut bacteria at three months old were more likely to show early signs of asthma.⁵ (See Skin Deep.)
• Autoimmune conditions, such as rheumatoid arthritis and type 1 diabetes, where the immune system attacks the body's own tissues. One gut bacterium, Prevotella copri, was found to be more common in people newly diagnosed with rheumatoid arthritis.⁶
• Type 2 diabetes and weight gain, explored further below.
• Low mood and depression. In a study of more than 1,000 people, two types of gut bacteria were consistently lower in those with depression.⁷
• Skin conditions, such as acne, eczema and rosacea, through what is sometimes called the gut–skin connection.

In many of these, scientists are still working out which comes first, the imbalance or the illness. But one example shows just how powerful restoring the gut can be. For people with repeated C. difficile infections, a transplant of healthy gut bacteria from a donor cured around nine in ten of them, compared with fewer than one in three treated with antibiotics alone.⁸

The gut–brain connection

Your gut and brain are in constant conversation, through the vagus nerve, hormones, immune signals and the compounds your microbes make. Most of the body's serotonin, a key messenger chemical, is made in the gut, and certain gut bacteria help control how much is produced.⁹ (See The Hormone Web.)

The link with stress is striking. In a well-known experiment, mice raised without any gut bacteria had an exaggerated stress response. When they were given healthy bacteria early in life, their stress response returned to normal.¹⁰ Research in people is still growing, but it is becoming clear that a healthy gut and a calm mind are closely connected.

The gut doesn't just digest your food. It helps shape how you feel, how you fight infection and how your body handles almost everything you eat.

Hormones, weight and metabolism

Your microbes also influence how your body handles energy. In one study, scientists took gut bacteria from pairs of twins, one lean and one with obesity, and gave them to mice. The mice that received bacteria from the twin with obesity gained more fat, even though they ate the same diet.¹¹

They help explain why the same food can affect two people so differently. When researchers measured the blood sugar of 800 people after identical meals, the responses varied enormously from person to person, and the make-up of each person's microbiome helped predict who would react in which way.¹² (See Balancing the Sugar Seesaw.)

One microbe has attracted particular excitement. Akkermansia muciniphila lives in the protective mucus layer that lines the gut, where it helps keep that layer thick and the gut wall strong. People with healthier blood sugar, cholesterol and body fat tend to have more of it, and in one study, those with higher levels gained more benefit from a weight-loss diet.¹³ In a small trial in people with excess weight and insulin resistance, a daily supplement of pasteurised Akkermansia improved insulin sensitivity and lowered cholesterol.¹⁴ The most natural way to encourage it is through food. Polyphenols, the colourful protective compounds in cocoa, dark chocolate, berries, pomegranate, grapes, cranberries and green tea, act as a kind of fertiliser for Akkermansia, both in animal studies and in people, although we each respond a little differently depending on the other microbes we carry.¹⁵ In laboratory tests, pure cocoa powder fed its growth directly. So a square or two of good dark chocolate is a treat your microbes enjoy too.

Gut bacteria even help manage hormones. A group of microbes, sometimes called the estrobolome, affects how much oestrogen is recycled back into the body rather than cleared away, which may matter for hormonal balance.¹⁶

Even your medicines

Your microbes can change how medicines work, too. One common gut bacterium can inactivate digoxin, a heart medicine, which helps explain why the same dose works differently in different people.¹⁷ It is another sign of just how far the microbiome's influence reaches.

What upsets the balance

• A low-fibre, highly processed diet, which starves the microbes that make butyrate.
• Antibiotics. Sometimes essential, but they can disturb the gut for months. In one study, some species were still missing six months after a course.¹⁸
• Long-term stress and poor sleep, which affect the gut through the gut–brain connection.
• A narrow diet, eating the same few foods day after day.

How to care for your inner garden

• Aim for 30 different plants a week. In a large study, people who ate more than 30 types of plant a week had more varied gut bacteria than those who ate 10 or fewer.¹⁹ Vegetables, fruit, beans, whole grains, nuts, seeds, herbs and spices all count.
• Feed them fibre. Oats, beans, lentils, onions, leeks, garlic, asparagus and slightly green bananas are favourite foods for your microbes.
• Enjoy fermented foods. In a Stanford study, people who ate more fermented foods such as yoghurt, kefir, sauerkraut and kimchi for 10 weeks developed more varied gut bacteria and lower markers of inflammation.²⁰
• Add colour. The polyphenols in berries, cocoa and dark chocolate, green tea, olive oil and herbs feed beneficial bacteria, including Akkermansia.
• Cut back on ultra-processed foods, and use antibiotics only when they're truly needed.
• Rest and move. Good sleep, time outdoors and regular movement all support a healthy gut.

At Rootwise, the gut is often where we begin. Through diet, lifestyle and, where helpful, microbiome testing, we look at how your gut may be affecting the way you feel, and build a plan to bring it back into balance.