The Gut Microbiome and Your Health: How It Affects Your Wellbeing

Understanding the importance of your gut microbiome is key to improving your overall health.

The way we process and absorb food varies from person to person. Have you ever wondered why some people can eat certain foods without issue, while others experience discomfort? For those following the Zoe program, you're already familiar with the concept of the gut microbiome. Everyone has a unique composition of species in their gut, primarily made up of two main groups: Bacteroidetes and Firmicutes, which account for around 90% of your microbiome.

What is the gut microbiome?

The gut microbiome refers to the trillions of bacteria, viruses, and fungi that live in your intestines. It’s not just a passive part of your digestive system — your microbiome plays a crucial role in your health. Your gut’s microbial composition is influenced by factors like diet, lifestyle, and other behaviours. In fact, studies suggest that the more diverse your microbiome, the better your overall health. A healthy microbiome is essential for:

• Strengthening the barrier of the gut to protect against harmful bacteria.
• Enhancing hormone secretion, which helps regulate sugar levels and appetite
• Producing essential vitamins
• Supporting immune system function
• Modulating fat storage and metabolism
• Promoting a healthy central nervous system

How the microbiome supports digestion, immunity, mood and heart health

Beyond the roles above, your gut bacteria break down dietary fibre into short-chain fatty acids that fuel the cells lining your gut and help regulate inflammation. The gut is also home to around 80% of the body’s immune cells, according to Cleveland Clinic, making it central to how you fight infection. Through the gut-brain axis, gut bacteria help produce neurotransmitters such as serotonin, linking gut health to mood and mental wellbeing. Certain gut bacteria can also produce a compound called TMAO, which has been linked to a higher risk of atherosclerosis and cardiovascular disease – one reason a healthy gut may support a healthy heart. For more on protecting your heart, see our guide to healthy hearts.

Gut dysbiosis: when things go wrong

When there’s an imbalance in your gut microbiome, known as gut dysbiosis, it can lead to serious health issues like obesity, cardiovascular diseases, multiple sclerosis, and autoimmune diseases. Factors that contribute to gut dysbiosis include:

• Lack of physical activity
• Overuse of antibiotics
• Poor diet, especially one high in processed foods
• Lack of sleep
• Chronic stress and mental health issues
• Chemical exposure

Conditions linked to gut dysbiosis

Gut dysbiosis has been associated with conditions including irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), small intestinal bacterial overgrowth (SIBO), and metabolic and cardiovascular risk factors such as type 2 diabetes – though these are associations rather than proven direct causes, and gut health is only one of many contributing factors.

Signs of an unhealthy gut

Common signs that your gut microbiome may be out of balance include:

• Bloating and excess gas
• Poor or uncomfortable digestion
• Lower abdominal pain
• Irregular bowel habits, such as constipation or diarrhoea
• Fatigue
• For some people, changes in mood

See a GP if these symptoms are severe, persistent, or come with unexplained weight loss, bleeding, or a change in bowel habit that lasts more than a few weeks, rather than managing them yourself.

How to improve your gut microbiome

There’s no single fix, but these evidence-based habits support a healthier balance over weeks, not days:

• Eat a wide variety of plants and aim for around 30g of fibre a day, per NHS guidance on digestive health
• Include fermented foods, such as live yoghurt or kefir
• Feed good bacteria with prebiotic foods – see Guts UK on gut bacteria for more
• Limit ultra-processed foods, added sugar and excess alcohol
• Prioritise sleep and regular activity
• Only use antibiotics when a GP or clinician prescribes them

Best foods for a healthy gut microbiome

Prebiotics are fibres that feed the good bacteria already living in your gut, while probiotics are live beneficial bacteria themselves – both play a part in a healthy microbiome.

Prebiotic foods:

• Artichokes
• Asparagus
• Garlic and onions
• Leeks
• Bananas
• Oats and other wholegrains
• Legumes

Fermented and probiotic foods:

• Live yoghurt
• Kefir
• Sauerkraut
• Kimchi
• Kombucha

Foods to limit for gut health

A few dietary habits tend to reduce microbial diversity – the aim is moderation rather than elimination:

• Ultra-processed foods and refined sugar
• Excess saturated fat
• Artificial additives
• Heavy alcohol use

Are gut microbiome tests worth it?

Commercial gut microbiome ("poo") testing kits claim to map the bacteria in your gut, but clinicians are generally cautious about them, because the science isn’t yet precise enough to turn a home test result into reliable personalised advice. If you have persistent gut symptoms, a GP can assess them directly and, where appropriate, arrange stool or breath tests to rule out specific conditions – a more useful next step than an unregulated home kit. For more on eating for gut and digestive health more broadly, see our nutritious guide to eating well.