Gut health is the topic on everyone’s lips. Unfortunately, that means with growing interest in this area, we’re seeing a rise in products and online advice that promise the world, but lack credible evidence and distract from what really matters. Think cleanses, detoxes, resets and daily supplements sold for “general” gut health and digestion.
Yet, good gut health is built on strong foundations, not quick fixes. At the centre of these foundations is the gut microbiome (GM). In most instances, this complex microbial ecosystem does not need detoxing or drastic resets – it needs consistent, science-backed support to stay balanced, diverse, and resilient.
Here, we unpack what the gut microbiome is, why it matters, how it’s affected by antibiotics or infections, and, most importantly, how to support it.
What is the gut microbiome?
From head to toe, you’re covered in microbes. Your thumb hosts roughly as many microbes as there are people in Scotland (1). But before you panic and reach for the hand sanitiser, the good news is that most of these microbes are beneficial - and in fact essential - to your health.
The gut is home to the home to around 100 trillion microbes, making it the most diverse microbial community in the body. Together, these microbes weigh about 1.5kg (2,3) which is roughly the same as your brain.
You might hear ‘gut microbiota’ used to refer to the microorganisms themselves, and ‘gut microbiome’ to describe the microorganisms plus their genetic material. For simplicity, we’ll refer to this whole ecosystem as the gut microbiome, or GM.
Why should we care about our gut microbiome?
Far from being freeloaders, the trillions of microbes in your gut are deeply involved in keeping you healthy. In fact, we likely couldn’t survive without them. Here's why:
They produce health-promoting substances
Dietary fibres (think vegetables, fruits, nuts, seeds, and wholegrains) are specific types of carbohydrates that cannot be broken down by the human body. Instead, fibre passes through to our large intestine, where our microbes are able to break them down for us (also called fermentation). As a by-product of microbial fermentation, our gut bacteria produce very small anti-inflammatory substances called short-chain fatty acids (SCFAs). These SCFAs, including butyrate, acetate and propionate, serve a range of health-promoting functions. Butyrate, in particular, is the primary fuel for the cells lining the colon, helping to keep the gut barrier strong and inflammation in check (4-6).
They support your immune system
Many scientists estimate that around 70-80% of your immune system is located in your gut, where they’re in constant communication with the GM (7). This interaction between the GM and the immune system helps ‘train’ the immune cells to know what to react to and what to ignore. This is why a well-balanced GM can better support the immune system to respond to threats like pathogens while staying tolerant to food and friendly bacteria – reducing the risk of illness, infection, or allergies (8). A recent study showed that children who live with more household pets in their first year of life are less likely to develop allergies later on, with the effect increasing the more pets they’re exposed to. It’s a phenomenon researchers call the “mini-farm” effect (9). While this does not guarantee protection for every child, it highlights how early-life exposure to a wider range of microbes can help shape our immune health.
They interact with your gut-brain axis
Your gut and brain are in constant conversation through a number of overlapping pathways involving the vagus nerve, hormones, the blood-brain barrier, and immune messengers (10). What we know so far is that maintaining a healthy GM is important for a number of brain functions – from how we process feelings of anxiety, sadness and stress, to how we connect socially with others (11). The GM has also been linked to how well we sleep (12), our ability to concentrate, and even our memory and rate of cognitive decline as we age. Importantly, the gut-brain connection is a two-way street. So when we are feeling anxious or stressed, this often leads to gut-related symptoms, including stomach pain, diarrhoea, bloating, and constipation.
They help balance hormones
While evidence is still emerging in this area, the GM is now recognised as playing a key role in regulating hormones, particularly oestrogen (13). Certain microbes produce enzymes (like β-glucuronidase) that influence how oestrogen is metabolised and recirculated in the body. A disrupted GM may interfere with this process, potentially contributing to hormonal imbalances, menstrual disturbances, or symptoms associated with perimenopause and the menopause. In practical terms, this means that supporting gut health may help the body manage hormonal changes more smoothly, rather than acting as a quick fix or cure for hormone-related symptoms.
They support metabolic health
Metabolic health refers to how well the body manages energy, including blood sugar control, insulin sensitivity, fat storage, and inflammation. A healthy GM contributes to metabolic health by helping regulate blood sugar levels, insulin sensitivity, and pathways involved in how the body stores fat. Evidence also suggests that SCFAs produced by gut microbes influence energy balance, appetite regulation, and fat metabolism (14). Some studies suggest that people with a more diverse and balanced gut microbiome tend to have better metabolic markers and may be less prone to conditions like obesity, insulin resistance, or type 2 diabetes (15). These relationships are complex and bidirectional, meaning metabolic health can also shape the GM over time.
They produce essential vitamins
While diet remains the primary and most reliable source of vitamins, the GM can act as a helpful supporting system. Certain gut bacteria help synthesise essential vitamins, including vitamin K (important for blood clotting and bone health) and several B vitamins, such as B12, folate, and biotin - all crucial for energy production, brain health, and red blood cell formation.
What disrupts the gut microbiome?
The GM is resilient, but it’s not invincible. There are a few common factors that can disrupt the balance.
Antibiotics
Antibiotics are essential in fighting infections, but they don’t discriminate. They wipe out the good and the bad bacteria. After a course of antibiotics, microbial diversity tends to drop significantly. Some beneficial bacteria may take weeks or even months to bounce back. Without careful planning, this disruption can lead to unwanted side effects, such as diarrhoea or increased vulnerability to gut pathogens15. Repeated or unnecessary antibiotic use can disrupt the GM over time, and these changes have been associated with a higher risk of some chronic health conditions. Starting on the first day of antibiotic treatment, consider taking a strain-specific live bacterial supplement to reduce the risk of antibiotic-associated diarrhoea (see here for more detail).
Infection
Infections caused by pathogens like C.diff, Salmonella, or Campylobacter can also wreak havoc on the GM. These infections can cause acute inflammation and disrupt the normal balance of microbes, reducing the abundance of beneficial species and allowing opportunistic organisms like pathogens to take over. Recovery from a gut infection often involves a period of microbial instability. For some, especially those with pre-existing dysbiosis or a history of antibiotic use, it may take a long time and targeted dietary or strain-specific live bacteria to help restore balance (16).
Low-fibre diets
Diets that dramatically limit fibre (e.g. the carnivore or keto diet) can rapidly reduce the diversity and activity of beneficial gut bacteria. Since our bacteria rely on fibre as their main fuel source, their populations reduce when fibre is removed from the diet. Over time, this can lead to a drop in the production of beneficial metabolites like butyrate, which we know plays a key role in maintaining the gut lining and regulating inflammation. Meaning that a low-fibre diet may also shift the GM toward a more proinflammatory profile, potentially increasing the risk of gut barrier dysfunction, inflammation, and metabolic dysfunction.
How do we measure gut microbiome health?
Gut health isn’t just about having the “right” bacteria. It’s about having a diverse, balanced, and functional microbial ecosystem. Researchers tend to look at three key indicators:
Diversity
A wider variety of microbial species is generally associated with better health and greater resilience. A diverse microbiome is more adaptable and better equipped to deal with stressors.
An abundance of beneficial bacteria
While research is ongoing, some bacteria, such as Faecalibacterium prausnitzii (17-18) and Bifidobacterium, are consistently associated with positive health outcomes, including reduced inflammation, increased short-chain fatty acid (SCFA) production, and a stronger gut barrier.
Metabolic activity
It’s not just who’s there, but what they’re doing that's important. A healthy GM produces beneficial metabolites like SCFAs (butyrate, acetate, propionate), which indicate active fibre fermentation (and positive effects on human health).
Ultimately, there’s no single "perfect" microbiome. Health comes from a stable, functional community of microbes working in harmony with you.
The 6 foundations of good gut health
A healthy gut doesn’t come from quick fixes or single supplements: it’s built on everyday habits that support your GM over time.
If you’re just starting out on your gut health journey, these six foundations form the basics for creating a resilient, balanced, and thriving gut microbiome.
1. Prioritise plant-based diversity
Aim for 30 different plant points each week (19) across what Dr Megan Rossi calls the Super Six ( vegetables, fruits, legumes, wholegrains nuts and seeds, plus herbs and spices). These offer different types of fibre, nutrients, and polyphenols, which your microbes love. Variety is more important than volume. A handful of different plants is better than a mountain of spinach alone.
2. Feed your microbes with prebiotics
Prebiotics are specific types of fibre that selectively feed your beneficial gut bacteria. You’ll find them in foods like garlic, onions, leeks, asparagus, Jerusalem artichoke, green bananas, oats, and legumes.
3. Exercise regularly
Early research shows that aerobic activity has been linked to increased microbial diversity and higher production of anti-inflammatory substances in the gut – like butyrate. Bonus points if you exercise in a forest or green space for that gut-brain connection!
4. Prioritise sleep
Research shows that the GM is closely linked to our circadian rhythm, the internal clock that helps the body know when to sleep, eat, and repair. Disrupted or insufficient sleep can alter microbial diversity and composition, which may affect metabolic, immune, and digestive health (20).
5. Manage stress
Chronic stress can disrupt the gut-brain axis and place ongoing strain on microbial health. Build stress management activities into daily life that can stick to in the long term, like mindfulness, deep breathing, a warm bath, or movement that you enjoy. In one study, people with acid reflux who practised slow, abdominal breathing experienced fewer symptoms, better sleep, and reduced reliance on antacids over time, highlighting how calming the nervous system can directly support digestion (21).
6. Consider live bacterial supplements when needed
Probiotics (aka live bacterial supplements) can support a healthy GM for specific cases using including:
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Supporting IBS symptoms
When it comes to live bacterial supplements, you need to be specific, using the right strain, at the right time, at the right dose. You can find the latest evidence and guidance on how to choose the right live bacterial supplement here.
References
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Written by Rachel Redman - Registered Dietitian
Reviewed by Josie Porter, Registered Dietitian
