Beat the Bloat Part 4: The Gut Microbiome

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It’s been a while since the last instalment in my series on bloating, mainly due to COVID-19 coming into the world and turning all our lives upside down. So before I set that right, let’s recap on what I’ve covered so far.

  • In Part 1, we looked at the ways in which you eat your food can make a difference, and that slowing down and eating mindfully can make a difference
  • Part 2 was all about lifestyle factors such as sleep and exercise that can contribute to or reduce bloating
  • In Part 3 we finally got around to food, discussing particular foods that commonly trigger bloating in susceptible people, and foods that tend to be calming

Before going on, it’s important to reiterate that persistent bloating that is not typical for you can be a symptom of ovarian cancer. Please always visit your GP to get any bloating that you are worried about checked out. For more information on the symptoms of ovarian cancer, click here.

That said, on to the subject of this instalment: the gut microbiome.

What is the gut microbiome?

The human digestive tract is naturally populated with billions of microbes: bacteria, archaea, yeasts and fungi, protozoa and viruses. I often describe the microbiome as being like a rainforest – there are a huge variety of species, many of them undiscovered. If one or two individual species of plant in a rainforest overgrew and dominated, other species would die off as a consequence, due to lack of room, sunlight or nutrients. The whole health of the ecosystem would change. So it is in our gut.

There are some microbes that we have evolved with which benefit us – these are the commensal, or “good” microbes.

There are some species that are fine if their numbers are kept in check, but which can overgrow and cause problems for our health if the conditions in our gut allow them to – these are called opportunistic microbes.

And then there are species which can cause problems in any amount – pathogenic microbes.

Each of us has our own unique microbiome. To a large extent we acquire the basis for our lifelong microbiome in the first few years of life, but it is also true that changes we make to our diets and lifestyles in later life can change our microbiome. As in any ecosystem, there are niches for different species. Microbes use nutrients from the food we eat to survive, so the type of diet we follow can influence which species can take up residence and thrive

We still have a lot to learn about the microbiome. However, it seems that the guts of healthy people have an abundant and diverse mix of commensal microbes. This helps to create an environment in which opportunistic bacteria are kept in check and pathogenic microbes don’t get a look in. A healthy microbiome is more resilient.


Dysbiosis is a term used to describe an imbalance in the gut flora. It can be caused by a number of factors, including:glass of wine

  • Use of antibiotics or other medications which kill off good bacteria, including chemotherapy
  • An infection such as food poisoning
  • Stress
  • Alcohol consumption
  • Poor digestion
  • The Western diet, high in sugars, refined carbohydrates, processed meats and low in fibre(1)

How does dysbiosis cause bloating?

As I mentioned above, bacteria survive by fermenting carbohydrates from our food. Gases are produced as a by-product. It is thought that “bad” bacteria, the type that thrive on a diet high in sugar and refined carbohydrates, may produce greater amounts of gas, causing bloating.

The presence of dysbiosis can affect the transit time of food through the gut, resulting in constipation. This by itself can cause bloating as there is increased time for bacterial fermentation of food to occur and extra waste bulk in the gut.

Sometimes it’s a case of bacteria or other microbes being in the wrong place. While the large intestine is naturally teeming with microbes, there shouldn’t be very many in the small intestine. If microbes overgrow in the small intestine then this too can cause significant bloating.(2)

What can I do about it?

  1. The first step to take is to create an environment in the gut in which the “good” microbes can thrive. Do this by eating a diet low in processed foods, sugars and refined carbohydrates, and high in vegetables, fruits, herbs and spices, nuts, seeds, pulses and whole grains. In other words, eat real food! This will provide fibre which the “good” microbes love to eat, and deprive the “bad” microbes of the sugars and processed foods they need to survive. If you do suffer from bloating, it’s best to increase dietary fibre slowly so that your gut can get used to it gradually – otherwise you could end up with a lot more gas and wind as you adjust!
  2. Foods that particularly encourage the growth of beneficial microbes are called prebiotics. Prebiotic foods include oats, flaxseeds, asparagus, brussels sprouts, lentils, Jerusalem artichokes, leeks, onions, garlic, stewed apples and seaweed. Gradually introducing more prebiotic foods into your diet will encourage microbial diversity.
  3. sauerkraut jarFermented foods actually contain beneficial microbes. Contrary to popular belief, these do not transfer to the gut and colonise it when we eat fermented foods, but they do influence the gut environment as they pass through. This helps encourage abundant commensal microbes. Fermented foods include kefir (fermented milk), kombucha (fermented green tea), sauerkraut (fermented cabbage) and kimchi (fermented vegetables, Korean style). As with prebiotics, take it slowly when you start consuming fermented foods and build up gradually.
  4. Another step you can take that can be very successful in combatting bloating caused by dysbiosis is to space your meals out and avoid grazing throughout the day. Allowing 4-5 hours without food between meals and at least 12 hours overnight may help to discourage the overgrowth of microbes in the small intestine which can cause bloating.

What if this doesn’t work?

If you try the steps above without much improvement, it may be worth digging a little deeper to find out what is going on in your gut. You might have a more serious imbalance such as a chronic infection with a pathogenic bacteria, parasite or yeast that needs to be dealt with. These are more common than you might think! It can also help to get an outside opinion to guide you towards the interventions which are likely to be helpful for you, avoiding a scattergun approach.

In my practice, I have access to functional medicine stool tests for my clients. These can provide a wealth of information on what is really going on in an individual gut (3). As well as information on the abundance and diversity of the commensal flora, a stool test can

  • Detect potentially pathogenic infections
  • Give information about the health of the immune system in the gut
  • Provide markers that would suggest that a more serious condition such as inflammatory bowel disease might be present
  • Detect deficiencies in digestion that may be impacting gut health

There’s a saying in Functional Medicine: “Test, don’t guess”. It is always possible for us to work together to resolve your gut issues by trying nutritional therapy interventions based on your symptoms and your story. However, if you have been struggling with gut problems for a while now or have tried various interventions without any success, then a stool test could take the (informed!) guesswork out of what is going on and help point us in the right direction.

I hope you’ve enjoyed this series on Beating the Bloat. Although bloating may be very common, that doesn’t mean that it’s normal. Bloating is a signal from your body that your gut needs a bit of attention, and it’s always best to pay attention to these signals. If you’re interested in finding out how working with me one-to-one could help improve your gut health, then do please contact me on 07876016972 or at to book a free, no obligation discovery call. My clinic is 100% online at present.


  1. Brown, K., DeCoffe, D., Molcan, E. et al. (2012). “Diet-Induced Dysbiosis of the Intestinal Microbiota and the Effects on Immunity and Disease”, Nutrients, 4(8), pp1095-1119. Available at (Accessed 12 May 2020).
  2. Menees, S. and Chey, W. (2018). “The gut microbiome and irritable bowel syndrome”, F1000 Research, Version 1. Available at (Accessed 12 May 2020).
  3. Casén, C., Vebo, H.C., Sekelja, M. et al. (2015). “Deviations in human gut microbiota: a novel diagnostic tool for determining dysbiosis in patients with IBS or IBD”, Alimentary Pharmacology and Therapeutics, 42(1), pp71-83. Available at (Accessed 12 May 2020).