They’re found in supplements, yoghurt, kefir and fermented foods, and they’re often marketed as the solution to digestive problems.

But there is another group of compounds that may be even more important for long-term gut health:

Unlike probiotics, which are living microorganisms, prebiotics are substances that selectively feed beneficial microbes already living in your gut.

Think of it this way:

Without the right fuel, even the healthiest microbes struggle to survive and thrive.

“You can’t rebuild a healthy garden by adding new plants if you never feed the soil.”

Kate Troup Naturopath

The International Scientific Association for Probiotics and Prebiotics (ISAPP) defines a prebiotic as:

“A substrate that is selectively utilised by host microorganisms conferring a health benefit.”

In plain English, a prebiotic is something your body cannot digest but your beneficial gut microbes can.

When these microbes ferment prebiotics, they produce compounds called short-chain fatty acids (SCFAs) including:

These compounds help:

While polyphenols are not technically classified as prebiotics, they behave in many similar ways. Research increasingly shows that polyphenols from foods such as berries, cocoa, pomegranate, olives and green tea can influence microbial diversity, support beneficial bacteria and contribute to short-chain fatty acid production.

One of the biggest misconceptions about gut health is that there is a single “best” prebiotic.

Different microbes prefer different food sources. The healthiest microbiomes tend to be those exposed to a wide variety of fibres, resistant starches, polyphenols and prebiotic compounds, rather than large amounts of any single prebiotic.

This is why dietary diversity is consistently associated with greater microbial diversity, and better long-term gut health.

One of the most fascinating discoveries in microbiome science is that human breast milk contains large amounts of specialised prebiotics called human milk oligosaccharides (HMOs).

What’s remarkable is that babies cannot digest HMOs. In other words, nature designed breast milk to nourish the baby’s microbiome as well as the baby itself.

Researchers are now studying supplemental HMOs for their potential benefits in adults, particularly in supporting beneficial bacteria and gut barrier function.

One particular HMO called 2′-fucosyllactose (2′-FL) has attracted significant attention.

This is where genetics becomes interesting.

The FUT2 gene determines whether someone is a “secretor” or “non-secretor.”

Secretors produce fucose-containing compounds in their saliva, mucus and intestinal lining. These compounds help provide food and attachment sites for certain beneficial microbes.

Non-secretors often have a different microbiome composition and may be more susceptible to certain gut-related issues.

This is one reason why FUT2 status can influence microbiome diversity and resilience.

Interestingly, supplemental 2′-FL is now available and is being studied as a way to support some of the beneficial microbial functions that FUT2 secretors naturally provide.

If you’ve had DNA testing and discovered you’re a FUT2 non-secretor, this is an area worth understanding.

This is one of the most common questions I hear in clinic.

They then conclude:

“Prebiotics don’t agree with me.”

But often this just isn’t the case and is in fact a helpful diagnostic clue.

A strong reaction to a prebiotic can be a clue that the underlying microbiome isn’t functioning as it should.

In other words, the reaction may be providing useful information about the state of your gut ecosystem rather than proving that prebiotics are inherently bad for you.