Why finding the right prebiotic fibre starts with knowing your gut

Prebiotics are some of the most powerful clinical tools we have for lasting, positive changes in the gut microbiome. So why do so many people feel worse when they start taking them, and how do you find the right one for your gut?

Prebiotic-rich foods: roasted red onions, globe artichokes and garlic.

Many of my clients have already tried different prebiotic fibres before they booked an appointment with me. Perhaps they tried PHGG, GOS, FOS, or inulin, but without knowing which one is right for them. Some may have tried a prebiotic fibre that isn’t actually suitable for their symptoms, or simply tried to increase prebiotic-rich foods.

Within days they may feel more bloated, more uncomfortable, more symptomatic than before. They might assume they’ve done something wrong, or that the supplement or foods cause them harm. Usually, that isn't the case, but clinically their gut's reaction it's really useful information. Counterintuitively, the increase in symptoms is usually a signal that their gut microbiome needs more prebiotics, not less. But they need to be introduced carefully and in a highly targeted way.

What are prebiotics?

Prebiotics are different types of fibre that selectively feed beneficial bacteria in the gut. Prebiotics help create the right environment for a healthier microbiome by encouraging the growth of beneficial bacteria. These produce helpful compounds such as short-chain fatty acids that support the gut lining, influence immune function and help regulate bowel habit.

They are found naturally in a wide range of plant foods, but the amounts needed to produce a large-scale effect are often difficult to achieve through diet alone, especially if you are finding certain foods are contributing to your symptoms. For this reason, many people benefit from using a prebiotic supplement as part of a broader gut health plan.

Most prebiotic powders can be mixed into water, smoothies, yoghurt, porridge, or even tea, depending on the product. The most important thing is consistency, as the benefits are generally seen when the fibre is taken regularly over time.

But as prebiotics nourish beneficial bacteria, they also produce gas, so for some people with microbiome imbalances, the result can be bloating, cramping, or a worsening of the very symptoms the fibre was meant to help. This is partly why the conversation about prebiotics and conditions such as IBS or SIBO is more nuanced than the internet tends to suggest.

There is also a less well-known complication. In some cases with a particular microbiome profile (often associated with IBS-C), prebiotics can indirectly increase bacterial populations that are already overgrown, leading to constipation and bloating, and in very rare cases certain prebiotics can also cause an overgrowth of other bacteria known as Prevotella. But the question is rarely whether prebiotics are beneficial. It’s whether this particular fibre, at this dose, is right for this gut right now.

Why microbiome testing is so useful

Microbiome testing can provide helpful insight into the different bacterial populations in an individual’s unique microbiome, including how they interact with each other and how they are likely to respond to prebiotics. Rather than making a broad recommendation based only on symptoms, testing can reveal whether certain beneficial bacteria appear to be low and whether the overall microbial balance suggests a particular prebiotic — or a combination — may be more appropriate.

This is especially useful because different fibres tend to support different parts of the microbiome. Some prebiotics are better known for increasing Bifidobacteria, while others may support butyrate-producing bacteria or help normalise stool consistency. Understanding that profile can make recommendations more targeted and more effective.

Just as importantly, microbiome testing should never be used in isolation. A detailed history is essential. Symptoms such as bloating, constipation, diarrhoea, abdominal pain, food tolerance, medication use, stress, and overall diet all help determine which prebiotic is likely to be best tolerated and most beneficial, what dose is needed and over what time period.

Why a detailed history is so important

Each of our treatment pathways starts with a First Consultation where we seek to understand the client’s hopes for Microbiome Analysis and explore their case history. Two people can present with very different gut symptoms — sometimes with the same diagnosis — but Microbiome Analysis might show they need a completely different treatment plan. Two individuals with constipation may benefit from different fibres that help improve motility and frequency. Others who struggle most with bloating and gas can find certain prebiotics impossible to introduce, at least at the beginning.

A detailed history helps identify these differences. It also helps us identify when a prebiotic should be introduced carefully or avoided altogether. This is particularly important in people with IBS, food sensitivities, or a history of poor tolerance to fibre supplements.

The right fibre depends on the right context

There is no single best prebiotic fibre for everyone. The right choice depends on a combination of symptoms, stool pattern, tolerance, diet, and microbiome findings.

Take six prebiotics that all support the growth of Bifidobacteria to a greater or lesser extent — PHGG, GOS, lactulose, acacia fibre, resistant starches and inulin. The right choice between them still depends on gut symptoms, the broader microbiome picture, the presence or absence of certain other bacterial populations, symptoms and diagnoses, food intolerances, dietary restrictions, religious or ethical considerations, budget, client preference, and the location of the client, because not all of these are easily accessible in every country.

The prebiotic isn’t chosen by its properties alone, it’s chosen by fit.

That is why personalisation is so important. A fibre that improves one person’s gut health might worsen another person’s bloating or bowel symptoms. By using microbiome testing and taking a thorough history, it becomes possible to select a prebiotic that matches the individual rather than relying on guesswork.

This approach also helps support better long-term results. When you are given a prebiotic that matches your microbiome profile, it is more likely to be tolerated consistently and integrated into a daily routine that supports overall gut health.

If you’ve tried prebiotic fibres and felt worse, it usually means there are microbiome imbalances to attend to. Before trying again, it would be valuable to understand what those responses are telling you about your gut microbiome.

If you’d like to explore what microbiome testing could tell you and how a personalised approach to prebiotics could support your gut health, you can book a First Consultation or an Exploratory Call with me.

Melody Mackeown is a registered Nutritional Therapist and Microbiome Analyst. Find out more about working with her here: Melody Mackeown | The Microbiome Group

REFERENCES

Gill SK et al (2021) Dietary fibre in gastrointestinal health and disease. Nat Rev Gastroenterol Hepatol 18: 101–116. https://doi.org/10.1038/s41575-020-00375-4

Dey K et al (2023) Daily consumption of galactooligosaccharide gummies ameliorates constipation symptoms, gut dysbiosis, degree of depression and quality of life among sedentary university teaching staff: a double-blind randomized placebo control clinical trial. Indian J Gastroenterol 42: 839–848. https://doi.org/10.1007/s12664-023-01435-8

van der Schoot A et al (2022) The effect of fiber supplementation on chronic constipation in adults: an updated systematic review and meta-analysis of randomized controlled trials. Am J Clin Nutr 116: 953–969. https://doi.org/10.1093/ajcn/nqac184