Your body is home to an astounding 40 trillion bacteria, the majority of which reside in your gut. Collectively, these bacteria are known as your gut flora. You might also come across the term “gut microbiome,” which encompasses not just bacteria but also fungi, protozoa, helminths, and viruses. Imagine your gut microbiome – and your skin, vaginal, nasal, and oral microbiomes – as teeming ecosystems where balance is key.
I often find that many of the people I work with have an imbalance – either too few of one type or too many of another type of bacteria affecting their health. These imbalances are often identified through detailed gut microbiome stool testing.
Why is Healthy Gut Flora Important?
Bacteria are often thought of as bad. And it’s true that some gut bacteria are “bad” in that they can cause diseases or inflammation.
However, what’s also important to understand is that not all bacteria in our gut are bad.
Some bacteria become problematic only when their populations become unbalanced. For instance, certain species can be highly inflammatory in large numbers, and an overgrowth of specific bacteria is linked to various autoimmune diseases.
Imagine your gut as a car park filled with spaces. We want the right cars (bacteria) in the right spaces to prevent unwanted cars (harmful bacteria) from taking over.
Gut microbiomes play a number of roles, including:
- Taking nutrients from the food we eat
- Supporting our immune function
- Digesting fibres and proteins
- Producing B vitamins essential for energy and detoxification by the liver, and vitamin K, critical for blood clotting and bone health.
- Protecting the body from harmful pathogens (disease-causing agents)
Researchers have discovered that animals without a microbiome do not develop a normal immune system, highlighting the importance of gut microbes in our health.
The microbes in our gut work together with our immune cells to reduce the risk of infection and disease. They help maintain the health of the gut barrier, which is critical as a compromised barrier allows unwanted substances into the bloodstream.
This can trigger an inflammatory immune response linked to various conditions, including food intolerances and autoimmune diseases such as Hashimoto’s or Rheumatoid Arthritis, often associated with “leaky gut.”
Gut Flora Imbalance Symptoms
Our bodies are pretty good at letting us know when something is wrong. The following are some signs that your gut flora is imbalanced:
- Digestive issues such as bloating, gas, constipation (which means not going to the toilet at least once a day, if not twice), loose stools, diarrhoea, reflux, burping, excessive wind or other digestive problems
- Regularly getting sick or suffering from chronic infections
- Mental health issues such as feeling anxious or depressed (there’s a strong link between the gut and mental health)
- Skin issues such as acne, psoriasis, rosacea, or eczema
- Suddenly developing food intolerances
- Feeling tired and exhausted often
- Unexplained weight gain or loss
- Fibromyalgia, M.E, Chronic Fatigue

Factors that cause the gut bacteria to get out of balance, which we call “dysbiosis” can result from factors such as stress, poor diet, lack of breastfeeding, C-section birth and antibiotic use.
How to Restore Healthy Gut Flora
Food is the main source of fuel for your gut microbes. Recent studies suggest that diet can change your microbes, which can impact your overall health.
If you’re experiencing symptoms of an unhealthy gut flora, it’s possible to heal it naturally.
Eat More Fiber and Fermented Foods
Feed your gut bacteria with whole grains such as brown rice, quinoa, millet, and buckwheat. Include nuts (avoiding peanuts due to high mould content), seeds, low-sugar fruits, and a variety of vegetables. Incorporate fermented foods like kimchi and sauerkraut that are labelled as raw or unpasteurised – these contain live bacteria beneficial for your gut.
Aim for 7, ideally 9, fist-sized portions of colourful vegetables each day, as the phytonutrients in these foods support good bacteria. However, if vegetables worsen symptoms like bloating or gas, you might be dealing with SIBO (Small Intestinal Bacterial Overgrowth), where bacteria from the large intestine have proliferated into the small intestine.
Cut Back on Sugar and Processed Foods
Reducing your intake of sugar and processed foods is crucial as they can disrupt gut flora balance and promote harmful bacterial growth. Opt for whole, nutrient-dense foods to support a healthy gut environment.
Take Probiotics and Prebiotics
Probiotics are live bacteria found in foods like kefir, kombucha, and organic miso, which help restore healthy gut flora balance. Pair them with prebiotic foods such as Jerusalem artichoke, onions, and garlic to feed the good bacteria and encourage them to flourish.
If you suffer from SIBO, you might find that certain prebiotic-rich foods exacerbate symptoms due to their fermentable fibres (FODMAPs). In such cases, prebiotic fibre powders like PHGG or GOS might be more tolerable.
Manage Stress
Incorporating relaxation techniques such as meditation, yoga, or deep breathing can significantly benefit your gut health. Alternate nostril breathing, in particular, supports the vagus nerve, which plays a critical role in connecting your gut and brain. Practice this technique for 2-5 minutes before each meal and periodically throughout the day to manage stress effectively.
Get Enough Sleep
A good night’s sleep is essential for good health in general, including gut health. We repair our bodies whilst we sleep and the best sleep is between the hours of 10 and midnight.
Exercise Regularly
Exercise can help promote a healthy balance of gut flora by improving digestion and reducing stress but don’t exercise too soon after your meal. A gentle walk straight after a meal can, however, help your digestive processes.
It might take a little experimentation to find what works for you since everyone’s gut is unique.
Foods to Avoid for Healthy Gut Flora
Whilst some foods can promote healthy gut flora, there are others that can disrupt the delicate balance of microorganisms in your gut. To keep your gut flora healthy, avoid or limit these foods:
- Sugar can promote the growth of harmful bacteria in the gut, leading to an unhealthy balance of gut flora.
- Processed foods are often high in unhealthy fats, sugar, and preservatives, which can disrupt gut health.
- Artificial sweeteners like aspartame and sucralose can have a negative impact on gut health, promoting the growth of harmful bacteria.
- Gluten (a protein found in wheat, barley, and rye) can cause digestive issues such as intestinal permeability and disrupt your gut flora.
- Dairy (anything from the milk of an animal) can be inflammatory for some people, particularly cow’s dairy. If eating dairy, sheep and goats are better or more tolerated options (think halloumi, feta, etc).
Need Some Help Restoring a Healthy Gut Flora?
A healthy balance of gut flora can improve digestion, support immunity, and even promote better mental health. By making simple changes to your diet and lifestyle, such as eating more fibre, reducing stress, and taking probiotics, you can restore a healthy balance of gut flora and alleviate symptoms of an unhealthy gut.
Remember, everyone’s gut is different, so it may take some experimentation to find what works best for you. But by incorporating some of the tips outlined in this post, you can get on your way to better gut health. If you’re still struggling with gut health issues, don’t hesitate to reach out for support. I offer FREE 30-minute wellbeing reviews where we can chat through your concerns, and I can give you some quick tips to help you get started. We can also discuss various options for how we can work together to help you achieve your health goals. Book your slot and start taking charge of your gut health!

