Gastroenterologist Dietitian Dr Sammie Gill answers your burning gut microbiome questions

What is considered a ‘healthy’ gut microbiome?

While there is no agreed-upon definition of a ‘healthy’ gut microbiome, it is commonly described as both compositionally diverse (i.e. containing many different microbial species), and functionally diverse (i.e. the ability to perform a wide range of functions).

Other defining features of a healthy gut microbiome include resilience which reflects its robustness, adaptability, and ability to recover from disruptions (such as antibiotics or infections).

What’s more, growing research has linked alterations (or shifts) in the gut microbiome to a wide range of chronic health conditions. This has led to the idea of ‘gut microbiome signatures’ where certain health conditions tend to show similar patterns in their gut microbiome composition.

For example, people with inflammatory bowel disease (IBD) often have lower levels of a bacteria called Faecalibacterium prausnitzii.

That said, these observations represent emerging patterns (or trends), not established certainty. It doesn’t mean all people with IBD have lower levels of Faecalibacterium prausnitzii, nor does it mean you’ll develop IBD if you have lower levels of Faecalibacterium prausnitzii.

Are there ‘good’ and ‘bad’ microbes?

How your gut microbes ‘behave’ depends on you. Prioritise them and they will prioritise you – it’s a reciprocal exchange.

Often, gut microbes are divided into ‘good’, ‘bad’ or ‘neutral’ (also known as ‘opportunistic’). But the reality is far more complex than that.

For example, ‘good’ microbes might start misbehaving if they’re not given the right environment to thrive.

Let’s take Akkermansia muciniphila as an example. This microbe is a specialist mucus degrader that carefully breaks down mucus that lines the gut wall in a controlled way. In return, it releases helpful compounds, such as short chain fatty acids (SCFAs).

That said, if degradation becomes excessive or uncontrolled, it can compromise this protective mucus layer - which serves as both a mechanical and chemical immune defence barrier – potentially leading to inflammation or infection.

Lab studies have shown that a low fibre diet can stimulate the growth of Akkermansia muciniphila, leading to them breaking down the gut’s mucus layer more than usual. In other words, when fibre is in short supply, mucus degradation ramps up.

Put simply, supplying Akkermansia muciniphila with fibre means supporting it to function optimally.

Can gut microbes of the same species be harmful and harmless?

Yes. A typical example would be Escherichia coli - better known as E.coli.

It’s true that some E.coli strains do cause infection, like enteropathogenic E.coli (EPEC) and enterohaemorrhagic E.coli (EHEC).

However, most strains of E.coli live harmlessly in the gut. In fact, E.coli is one of the first members to colonise the infant gut and establishes itself as a life-long resident. They offer health benefits, like producing vitamin K and vitamin B12.

Why is there so much talk around the gut and serotonin?

Around 95% of all serotonin is produced in the gut. Only 5% is produced in the brain.

Both ‘types’ of serotonin are the same – they are just produced in different places and by different cells. Saying that, gut-based serotonin cannot enter the brain because it can’t cross the blood brain barrier.

While scientists are still trying to figure out how gut-based serotonin might affect the brain, emerging studies in mice have shown that increased serotonin in the gut can influence the expression of serotonin receptors in the brain.

Do gut microbes ‘remember’?

It’s thought that gut microbes have an ‘biological memory’ – that is, they ‘remember’ past exposures (specifically fibre) and modify how they respond in the future.

What’s more, there is evidence that the gut microbiome can remember past infections and become more resistant to similar infections in the future.

What is the best way to nurture my gut microbiome back to health after antibiotics?

There is no ‘one’ standard approach to supporting your gut microbiome post-antibiotics.

One way is to consider taking specific types of probiotics during and for a week after an antibiotics course.

Another way is to focus on fibre, specifically foods that contain naturally occurring prebiotics such as onion, garlic, leeks, asparagus, Jerusalem artichoke, and banana.

If you enjoy fermented foods, include those too.

Are gut microbiome tests worth it?

If you’re curious about what’s happening in your gut, gut microbiome testing can tell you which microbes are living there and possibly what they’re doing (e.g. what compounds they are producing).

A key challenge of gut microbiome testing lies in the interpretation of the results, mainly because the science is still emerging and many questions remain unanswered.

It’s important to keep in mind that poo samples offer an indirect measure of what’s happening in your gut. Not only that but the types of microbes along a stool will vary. In other words, the result will vary depending on where you take the sample from.

What’s more, given the dynamic nature of the gut microbiome (it can change within 24-48 hours), the result of a gut microbiome test is only one snapshot in time. For example, if you took two tests a few days apart, you’d likely get a different result.

Also, while some gut microbes have been linked with certain health conditions (such as the IBD example above), it is important to note that gut microbiome tests cannot detect or diagnose a disease, nor can they reliably predict or indicate disease risk.

To add another layer of complexity, the way a poop sample is analysed also differs from company to company. Some offer ‘high level’ insights whereas others offer a deeper dive.

Finally, some gut microbiome testing companies are more scientifically sound than others and can generate deeper insights thanks to large databases of thousands of people.

What about poo transplants (or ‘crapsules’)?

You might be surprised to learn that poo transplants – also called faecal microbiome transplantation (FMT) dates back thousands of years where human poo was called yellow soup and used in people with severe diarrhoea.

Fast forward to today and FMT continues to be used in healthcare settings - including the NHS – for use in very specific scenarios.

For example, FMT is highly effective for treating recurrent Clostridium difficile (or C.Diff) infection. In fact, the cure rate is around 90%.

FMT remains an evolving area of research with testing expanding into other health areas, including gut-related conditions such as irritable bowel syndrome (IBS) and IBD. Despite this, the level of success seen in C. diff has not yet been replicated.

Summary

It’s undeniable that the gut microbiome plays a major role in shaping short and long-term health. That said, clear-cut or absolute answers about the gut microbiome are rare. At present, the most reliable approach to supporting your gut is through everyday lifestyle choices and giving your gut microbes the environment they need to thrive.

Sources

What defines a healthy gut microbiome?. Gut. (2024). Link.

Systematic review and meta-analysis of the role of Faecalibacterium prausnitzii alteration in inflammatory bowel disease. Journal of Gastroenterology and Hepatology. (2020). Link.

Breaking down barriers: is intestinal mucus degradation by Akkermansia muciniphila beneficial or harmful?. Bacteriology. (2025). Link.

Human-derived bifidobacterium dentium modulates the mammalian serotonergic system and gut–brain axis. Cellular and Molecular Gastroenterology and Hepatology. (2020). Link.

Ecological memory of prior nutrient exposure in the human gut microbiome. Multidisciplinary Journal of Microbial Ecology. (2022). Link.

Exploring the memory of the gut microbiome: a multifaceted perspective. Frontiers in Microbiomes. (2024). Link.

Fecal microbiota transplantation: Review and update. Journal of the Formosan Medical Association. (2019). Link.