Understanding and Improving
Your Gut Microbiome

See also: Organic Food

Each of us has billions, if not trillions, of microscopic organisms living in our guts. There are bacteria, viruses, fungi and protozoa (unicellular organisms). We tend to think of bacteria and viruses as bad, because they cause various infections. However, many of the microbes living in your gut are not just helpful, but actually vital to the way that our bodies function.

It is only relatively recently that we have come to understand that our gut microbes are not just passive inhabitants of our bodies, but actually a key part of our personal ecosystems. With this understanding has come an interest in knowing how to encourage the ‘good’ microbes, and discourage the ‘bad’ ones. This page explains more about the gut microbiome, and how to improve yours.

What is the Gut Microbiome?

The gut microbiome is the term used for all the microbes living in your gut—or technically, their genetic material.

What’s in a name?

Strictly speaking, the gut microbiome is actually the genetic material from all the microbes that live in your gut.

The correct term for the microbes themselves is microbiota. However, the two terms are often used interchangeably.

Each of us has a different microbiome: it is absolutely unique to the individual.

Even identical twins only share about 35% of their gut microbiome—and unrelated people tend to share around 30%. Your gut microbiome is affected by your genes, what you eat, whether you have taken antibiotics (recently or previously), your age, how you were born—and quite likely many other factors that we do not know.

Interestingly, we tend to share more of our gut microbiome with our romantic partners than anyone else, especially if we are cohabiting.

What’s more, when your relationship is closer, your microbiomes tend to be even more similar. This may be because we are more likely to share physical contact—and therefore microbes—when we feel closer.

The gut microbiome is estimated to contain around three million genes. To put that into context, the human genome contains around 23,000 genes.

A more diverse microbiome seems to contribute to better health.

People with less diverse microbiomes are more likely to develop conditions such as coeliac disease, inflammatory bowel syndrome, Type 2 diabetes, eczema, and certain forms of arthritis.

The gut microbiome is very adaptable because of the speed with which microbes reproduce: around 20 minutes per generation. This means that it is possible to both increase and reduce the diversity within a very short space of time.

The Role of the Gut Microbiome

Gut microbes are far more than just passengers within your body. They actually have several vital functions, including:

  • Helping to digest food, especially protein and fibre

    Our gut microbiome helps to extract the nutrients from what we eat. We cannot digest fibre ourselves, so without our gut microbes it would simply pass straight through—and indeed, this is what we used to think happened. Now, however, we know that our gut microbes break it down to provide short-chain fatty acids, which support gut health and reduce inflammation elsewhere in the body. There is more about this in our page What is Fibre?.

  • Making Vitamins B and K

    We cannot make vitamins ourselves, so we need to get them from our food, or with a bit of help from our gut microbes.

    There is more about these in our page on Vitamins.
  • Supporting a healthy immune system

    Mice that lack a microbiome do not develop a normal immune system. Your gut microbiome therefore plays an essential role in building a healthy immune system.

    Broadly speaking, your gut microbes seem to work with your immune system to protect you from infection.

    They certainly have a physical role in preventing infection: they compete for space with pathogens (harmful microbes) in your gut. This means that pathogens are less likely to be able to grow there, and make you ill.

    Your gut microbes also maintain the health of your intestines. They seem to play a particular role in maintaining the boundaries of the intestines, and preventing leakage.

    Good vs Bad Microbes

    The precise combination of microbes in your gut directly influences your health. This is because some are good for you, but others are harmful. People with more harmful microbes are more likely to be obese, and to develop autoimmune diseases. It is thought that this may be connected to gut health, and particularly whether the gut becomes ‘leaky’.

  • How your body handles different foods

    Your gut microbiome has a huge influence on how your body deals with different foods.

    In one study, two groups of mice were given microbiome ‘transplants’ from a pair of human twins, one obese, and one with a normal body weight. The mice were all given the same food, in the same amounts. However, the mice given the microbiome from the obese twin became obese.

    The level of blood lipids (fats in the blood) after a meal is more affected by your gut microbiome than by the food that you eat.

Food and the Gut Microbiome

Your gut microbiome therefore affects how you manage food. However, it is also directly influenced by what you eat.

Your diet can both improve and reduce the diversity of your gut microbiome, and therefore affect your health.

For example, mice who were fed a diet that contained very little fibre for 4 weeks had 60% less diversity in their gut microbes. Ultra-processed foods are also linked to higher levels of ‘bad’ microbes. Eating more plant-based foods can increase the diversity again.

Birth, breastfeeding and the gut microbiome

Even before birth, babies are starting to develop their gut microbiome.

The birth process is effectively a way to introduce the baby to more microbes, as they pass through the birth canal. The microbes in a pregnant woman’s vagina actually change in the weeks before delivery, and become more like the gut microbiome. This provides her baby with a ‘seeding’ of beneficial microbes. Children born by caesarean section tend to have a less diverse microbiome than children born by vaginal delivery.

Breastfeeding also supports the development of the gut microbiome. Oligosaccharides in breast milk act in the same way as fibre for everyone else in nurturing gut microbes—so much so that manufacturers are considering whether to add fibre such as inulin to formula milk.

Nature has therefore provided natural ways for babies to develop their gut microbiome.

However, even if you are unable to take advantage of these natural methods for whatever reason, it is still possible to help your child develop a thriving gut microbiome. Skin to skin contact is very good for this. The microbiome also expands enormously once children are weaned, especially if they are exposed to a wide variety of different plant-based foods.

Helping Your Gut Microbiome

It is clear that eating more plant-based and less processed food is good for your gut microbiome.

Professor Tim Spector, author of The Diet Myth, and a leading researcher into the gut microbiome, suggests five specific actions that you can take to increase the diversity of your gut microbes. These are:

  1. Eat 30 different plants each week

    Variety genuinely seems to be the spice of life for your gut microbes.

    Eating lots of plant-based and fairly unprocessed foods is good—but eating a wide variety is even better. Try to increase the number of different fruits, vegetables and grains that you eat in a week, rather than always sticking to the same tried-and-tested options. Add in some nuts or new pulses. Tim Spector suggests aiming for a fairly unscientific 30 different types, including grains, rice and potatoes.

  2. Make your plate more colourful

    Eating different coloured foods in a meal is more appetising—and can also be better for your gut microbes.

    Colourful plant-based foods are likely to contain plenty of fibre. They also contain polyphenols, which are especially good for the ‘good’ gut microbes. Try eating more berries, nuts, brightly coloured fruit, vegetables, extra virgin olive oil and dark chocolate.

    There is more about the importance of fibre in our page What is Fibre?
  3. Add some fermented foods

    Fermented foods contain live microbes, known as probiotics, and therefore boost your gut microbiota.

    Fermented foods include live yoghurt, artisanal cheeses (especially smelly ones), kimchi, kombucha, sauerkraut and kefir. Ideally, you should eat a small amount of fermented food every day—which may be easier to manage than larger quantities anyway.

  4. Stop snacking

    Having longer breaks between eating gives your gut microbes a chance to rest.

    It also allows some of them to clean out your gut a bit—essential for a healthy gut and strong immune system. If you can eat earlier a bit in the evening, and give your gut microbes longer to rest overnight, that will be even better.

  5. Reduce your intake of ultra-processed food

    This is the ‘flip side’ of eating more, and a wider variety, of vegetables.

    There is a link between eating highly processed foods and high levels of ‘bad’ gut microbes. Ultra-processed foods do not contain much fibre or other ‘food’ for our gut microbes. They also contain high levels of sugar and artificial sweeteners, which do not help the microbes at all. They may therefore damage your gut microbiome, and reduce its variety and ability to function.

    Stress and the Gut Microbiome

    Research has shown that when you are stressed, your physiological reactions affect your gut microbes.

    The microbiome becomes disturbed by your stress, and ceases to operate in quite the same way. This explains why you may experience abdominal cramps or bloating when you are stressed.

    However, this can also happen when you would not exactly describe yourself as stressed, just a little unsettled. These stress reactions are relatively small, but they can set off a big chain of events within your body.

A Final Thought

The precise content of your gut microbiome is entirely unique—which is why each of us has slightly different responses to foods of different kinds. Without analysing your gut microbiome, it is therefore impossible to say precisely what foods you should eat.

However, we do know that a more diverse gut microbiome is associated with better health.

We also know that we can encourage this diversity by eating a wider variety of plant-based foods, and less ultra-processed food, and perhaps adding some fermented products. It is a relatively easy change to make, but it could make a big difference to your health.