What does a healthy gut microbiome look like?

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The gut microbiome is home to trillions of different types of bacteria that are known to help with digestion, immunity, healthy ageing and even mental health.  

But what does a healthy microbiome actually look like? In a nutshell a healthy gut microbiome is balanced and diverse, packed full of beneficial bacteria such as Bifidobacterium, Lactobacillus and more, allowing your body to function at its best. 

This guide will explore what a healthy gut microbiome looks like, how to tell if yours is in good shape, and how to maintain and improve it. 

The gut microbiome 

The gut microbiome consists of a vast community of bacteria, fungi, viruses and other microorganisms that live within the digestive tract. These microbes play a major role in our health by: 

• Aiding in food digestion 
• Synthesising vitamins and enhancing the absorption of minerals 
• Producing important enzymes and nutrients 
• Supporting and boosting our immune system 
• Helping to protect against harmful bacteria and pathogens 
• Influencing our mood and mental health 
• Reducing our risk of chronic conditions

A well-balanced microbiome helps restore imbalances in gut bacteria (gut dysbiosis) which can lead to digestive issues, inflammation, chronic conditions and negatively affect both short and long-term health. 

A diverse array of microbes 

A healthy gut microbiome contains a diverse range of different types of bacteria that each play a different role in supporting our digestion and immunity. Greater diversity means better digestion, stronger immunity and an improved resistance to disease. 

A healthy balance of bacteria 

Beneficial bacteria help break down food, produce essential nutrients, and keep harmful microbes in check. While many would prefer a gut microbiome that contains only beneficial bacteria, an excess of these bacteria can actually lead to an imbalance. So-called 'bad' bacteria play an essential role in maintaining balance by preventing the overgrowth of any single type of bacteria. 

An overgrowth of harmful bacteria can lead to gut dysbiosis, an imbalance of the gut microbiome. This can lead to unpleasant symptoms such as bloating, diarrhoea, constipation, food intolerances, tiredness and if not addressed can increase the risk of chronic conditions. 

Good and bad gut bacteria both play their part in maintaining an overall balance within your gut. 

Efficient digestion and nutrient absorption 

Your gut microbiome plays a huge role in breaking down food and ensuring that nutrients from those foods are extracted and absorbed by the body. A healthy microbiome ensures: 

• Smooth digestion without bloating or other common symptoms 
• Proper absorption of vitamins and minerals 
• The production of short-chain fatty acids (SCFAs), which are important for gut health and overall wellbeing 

Production of short-chain fatty acids

SCFAs (short-chain fatty acids) are highly beneficial compounds made by your gut bacteria when they digest fibre. Some of the most important SCFAs are butyrate and propionate which can provide the following health benefits: 

• Strengthen the gut lining (preventing toxins from leaking into the blood stream, also known as leaky gut) 
• Reduce inflammation in the gut 
• Provide energy to the cells of the gut lining 
• Regulate our appetite and help reduce obesity 
• Regulate metabolism 

Without enough fibre in your diet, your gut bacteria won’t produce enough SCFAs, which can lead to poor gut health. A deficiency in SCFAs has also been linked to chronic conditions such as inflammatory bowel diseases, cardiometabolic disorders and colorectal cancer. 

A strong gut barrier 

A healthy gut microbiome protects the lining of the gut, preventing harmful toxins and pathogens from leaking through the gut wall and entering the bloodstream. This can lead to inflammation, immune system overreactions and increase the risk of food intolerances. 

Strong immunity 

It is estimated that 70% of our immune system is located in our gut. A healthy gut microbiome helps to boost and regulate the immune system. The gut and the immune system are in constant communication and work together to maintain a healthy balance in the body. 

Regular and comfortable digestion 

Signs of a healthy gut microbiome can be identified during the digestion process. Typically, a healthy gut microbiome can ensure: 

• Regular, well-formed bowel movements (1 - 3 times per day) 
• Minimal bloating, gas, or discomfort after eating 
• No frequent diarrhoea, or constipation 

Positively affecting our mood and mental health 

Your gut and brain are connected through the gut-brain axis. A well-balanced microbiome supports mental health by: 

• Producing serotonin, the "feel-good" hormone 
• Reducing stress and anxiety 
• Improving focus and mood 
• Improve our quality of sleep 

An imbalanced gut has been linked to mood disorders like anxiety and depression. 

Lower risk of developing chronic conditions 

An imbalanced gut microbiome (known as dysbiosis) doesn’t just affect digestion, it can contribute to the development of chronic diseases. Research has linked poor gut health to several long-term health conditions, including inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) 

Obesity and metabolic disorders 

• Gut bacteria influence how your body stores fat and metabolises blood glucose. 
• Certain bacteria promote fat storage, increasing the risk of obesity and metabolic syndrome. 

Heart disease 

• Poor gut health can increase the production of trimethylamine N-oxide (TMAO) which is produced by the gut and is linked to the development of cardiovascular diseases. 
• A balanced microbiome supports cholesterol metabolism and reduces inflammation, which are both important for cardiovascular health. 

Autoimmune conditions 

• Changes in the gut microbiome can cause the immune system to attack itself increasing the risk of autoimmune conditions like rheumatoid arthritis, multiple sclerosis and Crohn's disease. 

Skin conditions 

• Certain harmful bacteria such as Staphylococcus aureus have been linked to conditions such as Eczema. 

How do I know if my gut microbiome is healthy? 

Signs of a healthy gut 

If your gut microbiome is in good shape, you’re likely to experience: 

• Regular, comfortable digestion 
• No frequent bloating, diarrhoea, or constipation 
• Regular, firm bowel movements 
• Good energy levels 
• Clear skin 
• Strong immunity (fewer colds and infections) and a faster recovery time 
• Stable mood and mental clarity 
• Improved sleep quality 
• Healthy body weight 

Signs of an unhealthy gut 

If your gut microbiome is out of balance, you might notice: 

• Frequent bloating, gas, stomach discomfort or common digestive symptoms 
• Irregular bowel movements (constipation or diarrhoea) 
• Food intolerances or sensitivities 
• Low energy or fatigue 
• Brain fog or mood swings 
• Anxiety 
• Skin issues like acne or eczema 
• Frequent colds or infections 
• Disturbed sleep

Can I have an unhealthy gut but experience no symptoms? 

Even if your gut microbiome is imbalanced, you may not notice obvious digestive symptoms. Some individuals may have an overgrowth of harmful bacteria but don't experience bloating, diarrhoea, or discomfort. However, this silent imbalance can still manifest later in life and contribute to long-term health risks, such as: 

• Increased inflammation throughout the body, which can lead to joint pain, fatigue, and autoimmune issues. 
• A weakened gut barrier, allowing toxins and harmful bacteria to enter the bloodstream (a condition sometimes referred to as leaky gut). 
• Disruptions in the gut microbiome that can influence heart health, blood glucose levels, and mental well-being. 
• A higher risk of developing chronic conditions later in life. 

The importance of testing your gut microbiome 

The gut microbiome plays a huge role in so many different aspects of our health, such as regulating our immune system, digestion, nutrient absorption and protecting us from many chronic conditions later in life.  

Microbiome testing can give you valuable insights into what’s happening inside your body such as: 

• Identify harmful bacteria and their numbers 
• Identify imbalances in your overall microbiome 
• Understand your risk of developing chronic conditions 
• Understand how well your gut is synthesising vitamins, minerals and nutrients 
• Discover which foods to eat to fuel the good bacteria and starve the harmful bacteria 
• Give you the tools to support your gut and overall health in the long term 

With this information, you can make personalised changes to your diet and lifestyle to optimise your microbiome for better digestion, immunity, overall health and healthier ageing. 

How to maintain a healthy gut microbiome 

A gut-friendly diet 

Eat a variety of fibre-rich foods - Fibre feeds your good bacteria, helping them to thrive. Good sources include: 

• Whole grains: brown rice, whole wheat, barley, and bran.  
• Nuts and seeds: almonds, flaxseeds, and chia seeds.  
• Fruits and vegetables: pears, apples, oranges, carrots, and green leafy vegetables. 

Add fermented foods and probiotic-rich foods - Probiotic foods introduce beneficial bacteria into your gut. 

Add probiotics and prebiotics to your diet. Learn the difference between probiotics and prebiotics to understand how they can improve your overall gut health. 

Limit processed foods and sugar - Processed foods and excess sugar can feed harmful bacteria, leading to gut imbalances. Aim to: 

• Reduce fast food and ultra-processed snacks 
• Cut back on added sugars and artificial sweeteners 
• Choose whole, natural foods whenever possible 

Stay hydrated 

Water helps with digestion and keeps your gut microbiome in balance. Drink 6-8 glasses a day to support your gut health. 

To learn about what foods that are good for gut health, read our guide that details what types of foods are the best for supporting your gut health and why. 

Lifestyle changes 

• Manage stress 
• Regular exercise 
• Getting enough sleep (7–9 hours per night) 

Limit antibiotic use 

Antibiotics can kill both good and bad bacteria, leading to imbalances. If you need them: 

• Take probiotics during and after your course 
• Eat fibre-rich and fermented foods to help restore gut health 

If you want more ways to improve your gut health, take a look at our guide. 

Saskia's recommendations

A healthy gut microbiome is diverse, balanced, and supports digestion, immunity, and mental health. If you experience regular digestive issues, fatigue, or food intolerances, it might be a sign that your gut bacteria need some attention. 

By eating a fibre-rich diet, including probiotics, managing stress, and staying active, you can support a thriving gut microbiome and improve your overall well-being. 

If you're unsure about your gut health, consider a microbiome test to get personalised insights and recommendations for optimising your gut health.