The gut microbiome is home to trillions of bacteria and other microorganisms that help with digestion, immunity, healthy ageing and even mental health.
A healthy gut microbiome is balanced and diverse, packed with beneficial bacteria such as Bifidobacterium, Lactobacillus and many others, allowing your body to function at its best.
This guide covers the signs of a healthy gut microbiome, 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 collection 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 the immune system
- Helping to protect against harmful bacteria and pathogens
- Influencing mood and mental health
- Influencing long-term health
When those microbes fall out of balance, digestive symptoms, inflammation and longer-term health problems can follow. A well-balanced microbiome keeps things running as they should.
A diverse array of microbes
A healthy gut microbiome contains a wide range of different bacteria that each play a different role in supporting digestion and immunity. Higher microbial diversity is generally considered a marker of good gut health, and lower diversity has been observed in people with a range of long-term conditions [1].
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 a part 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 and tiredness.
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 helps break down food and extract the nutrients your body absorbs. A healthy microbiome supports:
- 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 beneficial compounds made by your gut bacteria when they ferment fibre. The best-studied SCFAs, including butyrate and propionate, are thought to [2]:
- Strengthen the gut lining (preventing toxins from leaking into the blood stream, also known as leaky gut)
- Help regulate inflammation in the gut
- Provide energy to the cells of the gut lining
- Play a part in appetite and metabolism signalling
Without enough fibre in your diet, your gut bacteria won’t produce as many SCFAs. Lower SCFA production has been linked in research to conditions including inflammatory bowel disease and cardiometabolic disorders, although cause and effect are still being worked out [2].
A strong gut barrier
A healthy gut microbiome supports the lining of the gut, which keeps harmful toxins and pathogens from passing through the gut wall into the bloodstream. When the barrier is compromised, inflammation and immune reactions can follow.
Strong immunity
An estimated 70-80% of the body's immune cells are found in the gut [3]. A healthy gut microbiome helps train 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 supports:
- Regular, well-formed bowel movements. Anywhere from three times a day to three times a week is generally considered normal [4]
- Minimal bloating, gas, or discomfort after eating
- No frequent diarrhoea or constipation
A healthy gut-brain connection
Your gut and brain are connected through the gut-brain axis. Much of the body's serotonin, a chemical messenger involved in mood and digestion, is made in the gut, and research shows that gut bacteria help regulate its production [5]. Researchers are investigating how the microbiome relates to mood, sleep and mental health, and an imbalanced gut has been associated with anxiety and depression, although the direction of that relationship is not yet clear.
Lower risk of developing chronic conditions
An imbalanced gut microbiome (known as dysbiosis) doesn’t just affect digestion. 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.
- Differences in gut bacteria have been observed between people with and without obesity and metabolic syndrome.
Heart disease
- Some gut bacteria produce a compound called trimethylamine N-oxide (TMAO) from certain foods. In a study of just over 4,000 people, higher blood TMAO levels were associated with a higher risk of heart attack and stroke [6].
- A balanced microbiome supports cholesterol metabolism and helps regulate inflammation, which are both important for cardiovascular health.
Autoimmune conditions
- Changes in the gut microbiome have been observed in autoimmune conditions like rheumatoid arthritis, multiple sclerosis and Crohn's disease, although researchers are still working out whether these changes are a cause or a consequence.
Skin conditions
- Certain harmful bacteria have been linked to skin conditions. Staphylococcus aureus on the skin, for example, increases during eczema flares and tracks with how severe they are [7].
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, well-formed bowel movements
- Good energy levels
- Clear skin
- Fewer colds and infections, and a faster recovery when you do get them
- Stable mood and mental clarity
- Good sleep quality
Signs of an unhealthy gut
If your gut microbiome is out of balance, you might notice:
- Frequent bloating, gas, stomach discomfort or other 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 people have an overgrowth of harmful bacteria without bloating, diarrhoea, or discomfort. A silent imbalance can still matter, because over time it may contribute to:
- Increased inflammation throughout the body
- A weakened gut barrier, allowing toxins and harmful bacteria to enter the bloodstream (a state sometimes referred to as leaky gut)
- Disruptions that may influence heart health, blood glucose levels, and mental wellbeing
The importance of testing your gut microbiome
The gut microbiome touches many different aspects of health, from immunity and digestion to nutrient absorption.
Microbiome testing shows you the current state of your microbiome, including:
- Which bacteria are present, and in what numbers
- Imbalances in your overall microbiome
- How well your gut is equipped to synthesise vitamins, minerals and other nutrients
- Which foods feed your beneficial bacteria, and which feed the harmful ones
A test shows what is happening in your gut today. It does not diagnose any condition or predict future disease, and it is not a substitute for seeing a GP about symptoms. What it gives you is a clear picture to act on, so you can make personalised changes to your diet and lifestyle to support better digestion, immunity and overall health.
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. Fermented foods such as live yoghurt, kefir and sauerkraut contain live cultures.
Understand prebiotics and live cultures. Learn the difference between probiotics and prebiotics to understand how they fit into a gut-friendly diet.
Limit processed foods and sugar. Heavily processed foods and excess sugar can feed harmful bacteria, contributing 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 things moving through the gut. Around 6-8 glasses a day is the usual NHS guidance.
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)
Antibiotics and your gut
Antibiotics can reduce both good and bad bacteria, which can leave the microbiome temporarily out of balance. Always take antibiotics exactly as prescribed and finish the course; never skip or cut short a prescribed course to protect your gut. While you recover, fibre-rich and fermented foods can help support the microbiome as it re-establishes itself.
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 fermented foods, managing stress, and staying active, you can support a thriving gut microbiome and improve your overall wellbeing.
If you're unsure about your gut health, consider a microbiome test to get personalised insights and recommendations for optimising your gut health.
When to see a GP
Gut symptoms are usually harmless, but some need proper investigation rather than a test or a diet change. See your GP if you notice:
- Blood in your stool
- Unexplained weight loss
- A change in your bowel habit lasting more than three weeks
- Difficulty swallowing or persistent vomiting
- New, persistent gut symptoms starting over the age of 50
- A family history of bowel or ovarian cancer alongside gut symptoms
Sources
- Valdes AM, et al. Role of the gut microbiota in nutrition and health. BMJ, 2018.
- Koh A, et al. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell, 2016.
- Wiertsema SP, et al. The interplay between the gut microbiome and the immune system. Nutrients, 2021.
- Chen LY, et al. Normal bowel habits and prevalence of functional bowel disorders in Singaporean adults. Singapore Medical Journal, 2000.
- Yano JM, et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell, 2015.
- Tang WHW, et al. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. New England Journal of Medicine, 2013.
- Kong HH, et al. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Research, 2012.
