The gut microbiome: a user's manual

Tens of trillions of microbes live in your gut, and together they make up your gut microbiome. Here is who they are, what they do, and how everyday food choices shape them.

Who lives down there

Your gut is home to tens of trillions of bacteria, recent estimates say around 38 trillion, roughly as many as the cells in the rest of your body, and together they weigh about 200 grams. Across all of humanity researchers have found well over a thousand species, and each of us hosts a few hundred of them. Most live in the large intestine. Everyone's mix is different, shaped by how you were born, what you eat, where you live, and the medicines you have taken.

What they do

These microbes are busy. They break down fibres your own body cannot digest, produce certain vitamins including K and some B vitamins, interact with the immune system, and make short-chain fatty acids that the cells lining your colon use for energy. Researchers are also studying how they communicate with the brain, but that is a story for another article.

Diversity is the thing

If there is one word researchers keep coming back to, it is diversity. A varied microbiome is generally considered a more stable one. Diet is one of the biggest influences on it, and varied, plant-rich, fibre-rich eating is linked to a more diverse microbiome. Fermented foods are part of many traditional diets too: they contain live cultures, and how they interact with the gut microbiome is an active field of research.

What shapes it the other way

Studies associate a less diverse microbiome with a diet built on ultra-processed food and low in fibre, as well as with antibiotics, ongoing stress and too little sleep. Some of that is outside your control, and antibiotics are sometimes exactly what you need, but food and routine are largely in your hands.

How to feed it well

The advice is refreshingly unglamorous.

• Eat many different plants across the week, not the same three on repeat.

• Include fibre at most meals, since that is what many gut microbes feed on.

• Add a little fermented food to your plate, a forkful of kimchi, a glass of kombucha.

You cannot see your microbiome, but you feed it three times a day. Small, steady choices matter far more than any single so-called superfood.