How to feed your gut microbiome in 2021

One of the key determinants of your gut microbiome health is diet, so what should you be eating to nourish yours? 

The world inside your gut

In the late 17th century, Dutch scientist Antonie van Leeuwenhoek was observing water under a microscope when he noticed that it was teeming with tiny moving organisms. His discovery was in fact the first human observation of microbes, and his later descriptions of the different microbes found in oral and faecal samples set the scene for microbiome research.

Fast forward a few centuries and we now know that microbes live everywhere – on us, around us, and inside us too. In fact, your body is home to a complex microbial ecosystem which works tirelessly to protect you from illness, support digestion and mood.

bowl of porridge with microbes

The human gut is one of the most complex and abundant ecosystems with trillions of microbes (and their genes) that live in your gut. Since they’re too small to be seen by the naked eye, they can be imagined as a sort of invisible organ.  And, just like an organ, they are integral to your health.

Amongst their many jobs, these commensal microbes form an important part of your immune system. They line your gut like doormen, interacting with the contents that flow through the gut and blocking harmful species from taking up residence by competing with them for nutrients and secreting specific antimicrobial proteins which ‘kill’ other bacteria, including unwanted invaders.

Outside of their role in immune function, microbes aid digestion, turning indigestible dietary fibres into compounds known as short chain fatty acids (SCFA) which keep the lining of the gut healthy. (Read more on the contribution of microbes to nutrition here.) Microbes also communicate with the brain via various neurotransmitters (chemical messengers) that they produce, with research suggesting these play a role in mood regulation and stress reactivity – this is often discussed as the gut-brain-skin axis.

Caring for your gut microbes

One of the key determinants of gut microbiome health is diet (we recently covered this linked to a mother’s gut microbiome). When you eat, you’re not just feeding yourself but your microbes too. So, what should you be eating to feed these helpful residents?

The most important nutrient is fibre. Fibre is a type of carbohydrate found in plant foods – think fruits and vegetables, nuts, seeds, wholegrain cereals, and pulses. Unlike other types of carbohydrate, humans can’t digest fibre – which is resistant to our digestive enzymes – and so it moves through the gut sweeping waste along with it, ending its journey in the large intestine (or colon) where it’s fermented by microbes for energy. In fact, your gut microbes thrive on fibre – consider it a sort of fertiliser which keeps them well fed.

As well as plenty of fibre, eating a wide variety of plant-based foods seems important. In a 2018 study of healthy adults, McDonald and his team found that those who consumed about 30 different types of plant foods a week had more diversity in their gut microbiomes than those eating 10 or fewer. A greater microbial diversity is beneficial to human health as it allows more varied and flexible responses to environmental changes. The study also showed that the group with a more varied diet had fewer genes associated with antibiotic resistance – a global threat to public health.

Prebiotics are specific types of dietary fibre which have been linked with gut microbiome health. Prebiotics selectively stimulate the growth of beneficial microbes – in short, they are ‘food’ for bacteria. They’re found in various plant foods (see ‘what to eat’) but can also be consumed as supplements.

When you eat, you’re not just feeding yourself but your microbes too.

Did you know that the terms dietary fibres and prebiotics are sometimes used interchangeably? While prebiotics are types of fibre that selectively ‘feed’ gut bacteria that have beneficial functions, fibres are defined by their inability to be digested or absorbed in the small intestine and are not always prebiotic. However, we need both fibre and prebiotics in our diet for gut health.

Along with prebiotics, probiotics can support gut health when consumed. Scientists describe probiotics as live microbes which can benefit the health of the person taking them, when consumed in large enough quantities. They do this by supporting the gut bacteria that live in our guts and helping to keep harmful microbes in check. Probiotics can be taken as supplements, but some foods (like live yoghurt and fermented foods) also contain live microbes – although it’s not yet clear whether these contain sufficient levels to be termed probiotic.

Read more on prebiotics and probiotics here.

So, what to eat?

Here are my top picks, along with tips on how to include them in your diet.

Fibre superstars

In the U.K., the recommended fibre intake is 30 grams a day, but most of us eat far less than this – dietary studies suggest the average intake is closer to 19 grams. All fruits, vegetables, wholegrains, nuts, seeds, and pulses contain fibre – but the only way to know how much you’re getting it to keep a diary for a day or two and total up your intake. If you decide to increase your fibre intake, do so gradually to give your gut time to adjust. It is also important to drink plenty of fluid, as this helps fibre move through the gut.

Top fibre picks: bananas, sweetcorn, apples, raspberries, baked potato (skin on!), oats, lentils, chickpeas, rye bread, wholewheat pasta, linseeds, chia seeds


Prebiotics are specific types of dietary fibre which selectively stimulate the growth of beneficial microbes in the gut. They’re found in a range of plant foods – some are listed below. Try printing the list and add some of these foods to your shopping list each week.

Top prebiotic picks: Jerusalem artichoke, asparagus, greenish banana, garlic, onion, leeks, oats, cooked and cooled potato, pulses, barley


Fermented foods are made or preserved using live, beneficial microbes. Some fermented foods retain these microbes which may contribute to a healthy gut microbiome. However, as aforementioned some of these foods may be mis-classified as probiotic and more research is needed to determine their effect on health as there are few high-quality studies. To date, cultured dairy products (like kefir) have been shown to have higher levels of live microbes than other fermented foods.

Foods to try:

  • Milk kefir – similar to yoghurt, milk kefir has a tangy creamy taste. Try it is a smoothie, make a dressing for salads, or pour over muesli
  • Live yoghurt – use to top curries, stews, or breakfast cereal
  • Sauerkraut – krauts are great for adding to salads. Don’t be limited to traditional sauerkraut, you can ferment most vegetables and rotate flavours with the seasons. A spring kraut with green cabbage, orange and ginger is as delicious as a winter kraut with red cabbage and beetroot  
  • Kimchi – A Korean fermented pickle that adds punch to any dish. Try on top of rice, with eggs, or in a wholegrain sandwich with some mature cheddar or smoked tofu
  • Kombucha – A great alcohol-free options, or a grown-up low sugar alternative to a fizzy drink


Bircher Muesli with Kefir

Bircher muesli was developed Swiss physician Dr Bircher-Benner. It’s a tasty combination of fibre rich soaked oats and grated apple that sits in the fridge overnight ready for a grab and go breakfast. If you don’t have kefir, use live yoghurt instead.

Ingredients – serves 2 

  • 30 grams almonds
  • 1 large apple
  • 60g jumbo oats
  • 100ml apple juice
  • 160ml kefir
  • 30g sultanas
  • 0.5 tsp cinnamon


  1. Gather all your ingredients. Roughly chop the almonds and grate the apple into a large bowl.
  2. Add all of the ingredients to the grated apple and stir. Don’t worry if it looks like it is too much liquid, the oats will soak this up overnight. Simply mix together, cover and place in the fridge overnight
  3. In the morning, stir gently and add a little extra yoghurt if needed to loosen. Spoon the muesli into a bowl and enjoy!

Quick Red Lentil & Coconut Dahl

Split red lentils are a staple item for your pantry – not only are they rich in fibre, they cook quickly too. In this speedy dahl they’re combined with warming spices, prebiotic onion and garlic and coconut milk for a comforting lentil stew. 

Ingredients – serves 3-4

  • 2 onions, chopped
  • 4 cloves of garlic, chopped
  • 1 tbsp coconut or olive oil
  • 1 tsp dried ginger
  • 1 tsp ground coriander
  • 1 tsp chilli powder
  • 2 tsp turmeric
  • 1 aubergine roughly chopped
  • 1 mug split red lentils
  • 1 can chopped tomatoes
  • 1 can light coconut milk
  • 500ml vegetable stock
  • Juice of half a lemon
  • Chopped coriander and live yoghurt to serve (optional)


  1. Chop the onion and garlic. Heat the oil in a large non-stick pan and fry the onion and garlic for a few minutes until golden. Tip in the spices and continue to cook for a minute or two until they become fragrant.
  2. Tip in the lentils, aubergine, chopped tomatoes, coconut milk and veggie stock. At this point there is going to look like there is a lot of liquid. Don’t panic -the lentils are going to absorb all of it quite quickly
  3. Give everything a good stir and bring to a simmer and then turn down the heat until it’s barely bubbling and cook for 15-20 minutes until the liquid has been absorbed by the lentils and you have a creamy, thick texture. Whilst it’s cooking give it a good stir every five mins or so to make sure nothing is sticking.
  4. Once ready, check for seasoning and squeeze in the lemon juice if you have it.
  5. Serve over rice or with wholewheat pitta, topped with yoghurt and coriander

Flaxseed crackers

These crispy crackers are made entirely from flaxseed (also known as linseed), a small, flat, high fibre seed which has a nutty taste. It’s probably the easiest recipe you’ll come across – with the shortest ingredients list!

These crackers go brilliantly with a bit of cheese and Dearbhla Reynold’s Fermented Tomato Salsa – (which is a wonderfully easy ferment, just google the name to find the recipe), hummus or labneh and herbs.


  • 200 grams of flaxseed – golden or brown
  • 180ml water
  • Flavourings: a small amount of sea salt, rosemary or chilli flakes


  1. Pour the seeds into a bowl and add the water  and seasoning. Stir to submerge the seeds and ensure there are none stuck around the side of the bowl. Cover, place in the fridge and leave overnight
  2. Preheat your oven to 100C and line a baking sheet with parchment.
  3. Take the flaxseeds out of the fridge – they should have formed a gelatinous mass – which you can tip out onto the parchment.
  4. Use a spoon or a spatula to spread the linseeds out into a thin layer, a few millimeters thick. Use a knife to even up the edges and mark the entire rectangle into squares
  5. Place in the oven and bake for 3 hours
  6. Leave to cool slightly and then cut into squares. Leave to cool completely before storing.

Please note that the foods, recipes, and advice outlined above are suitable for those without existing gut health conditions or allergies who are looking to nurture their gut health. For those with an existing gut condition (such as IBS or gluten intolerance) eating more fibre and prebiotics may aggravate symptoms. It is important that we take a holistic approach to maintaining a truly healthy diet.


Luke K Ursell, Jessica L Metcalf, Laura Wegener Parfrey, and Robert. Knight. (2012). Defining the Human Microbiome. Nutrition Reviews, 70(Suppl 1), 1–12.

 Li, S., Mason, C., & Melnick, A. (2016). No Vacancy: How beneficial microbes cooperate with immunity to provide colonization resistance to pathogens. Current Opinion in Genetics and Development, 36(1), 100–106.

So, D., Whelan, K., Rossi, M., Morrison, M., Holtmann, G., Kelly, J. T., Shanahan, E. R., Staudacher, H. M., & Campbell, K. L. (2018). Dietary fiber intervention on gut microbiota composition in healthy adults: A systematic review and meta-analysis. American Journal of Clinical Nutrition.

McDonald, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., Goldasich, D., Dorrestein, P. C., Dunn, R. R., Fahimipour, A. K., Gaffney, J., Gilbert, J. A., Gogul, G., Green, J. L., Hugenholtz, P., … Kosciolek, T. (2018). American Gut : an Open Platform for Citizen Science. 3(3), 1–28.

Keep exploring

You have Successfully Subscribed!