What Your Gut Actually Needs: Prebiotics, Fermented Foods & the Microbiome

Nutritional Literacy: What Your Gut Actually Needs

Simon Hill, MSc, BSc, is a nutritionist, host of The Proof Podcast, and co-founder of 38TERA.

4 min read

There's a lot of noise in the nutrition space right now. Everyone has an opinion on what you should eat, which supplements to take, and what the latest superfood is. But when it comes to your gut — home to roughly 38 trillion microbes — the science points us toward two powerful, accessible strategies: prebiotics and fermented foods.

Let me break this down.

Prebiotics: Feeding Your Inner Ecosystem

Your gut microbes aren't passive passengers. They're metabolically active organisms that, when properly nourished, reward you by producing drug-like compounds — most notably short-chain fatty acids (SCFAs) like butyrate, propionate, and acetate. These molecules influence everything from immune regulation and gut barrier integrity to brain health and metabolic function. They are genuinely some of the most important compounds your body has access to, and you can't make them without your microbes.

So what feeds these microbes? Prebiotics. And this term extends well beyond what most people think. There are three key categories worth knowing:

Fibre — the classic prebiotic

Found abundantly in legumes, whole grains, vegetables, fruits, nuts, and seeds. Most people eating a Western diet consume around 15 grams per day when they should be aiming for 30 grams or more. This is the foundational fuel for your gut microbiome.

Resistant starch

A type of starch that resists digestion in the small intestine, arriving intact in the colon where it becomes a feast for your microbes. You'll find it in cooked and cooled potatoes, oats, green bananas, and legumes. It's one of the most potent drivers of butyrate production.

Polyphenols

Plant compounds found in colourful fruits and vegetables, extra virgin olive oil, tea, coffee, cocoa, and herbs and spices. Around 90% of polyphenols consumed are not absorbed in the small intestine and instead travel to the colon, where they act as prebiotics and are transformed by gut bacteria into bioactive metabolites. These compounds have been shown to promote the growth of beneficial bacteria and inhibit pathogenic species.

When you eat a diverse, whole food, plant-rich diet, you're delivering all three of these prebiotic categories to your gut microbes simultaneously. And in return, they produce the SCFAs and other metabolites that keep you healthy. It's a beautiful symbiotic relationship.

Fermented Foods: A Shortcut to Microbiome Diversity

While prebiotics feed the microbes you already have, fermented foods appear to do something different — they help expand the diversity of your microbial community.

The landmark evidence here comes from a 2021 study published in Cell by Justin Sonnenburg, Erica Sonnenburg, and Christopher Gardner at Stanford University. They randomised 36 healthy adults into two groups: one increased their consumption of high-fibre foods, the other increased their intake of fermented foods — things like yoghurt, kefir, kimchi, sauerkraut, kombucha, and fermented cottage cheese — for 10 weeks.

The results were striking. The fermented food group experienced a steady increase in gut microbiome diversity and a significant reduction in 19 inflammatory markers, including interleukin-6, a key driver of chronic inflammation. The high-fibre group, surprisingly, did not see the same cohort-wide increase in microbial diversity over the study period. But when the researchers looked more closely, they found something important: it was the participants with low baseline microbiome diversity who struggled to respond to the increased fibre. Those with already diverse microbiomes adapted well.

This matters because many people in industrialised societies have depleted gut microbial communities — potentially due to a history of antibiotic overuse, diets high in ultra-processed foods and low in fibre, C-section birth, or other factors that reduce microbial diversity over time. For these individuals, simply adding more fibre overnight may overwhelm a gut that doesn't yet have the microbial machinery to break it down. The takeaway isn't that fibre doesn't work — it's that some people may need to dial up fibre more gradually, giving their gut time to adapt and recruit the microbes needed to fully reap the benefits of a high-fibre diet. This is also where a complete, low-FODMAP certified prebiotic supplement like DMN can be particularly helpful. Unlike most prebiotic supplements that only include one type of prebiotic, DMN delivers all three — fibre, resistant starch, and polyphenols — offering a way to consistently nourish your gut microbes across the full spectrum of prebiotics and build microbial capacity without the bloating or discomfort that can come from rapidly increasing dietary fibre alone.

This is an important nuance. Fermented foods may offer a faster, more universally accessible route to increasing microbial diversity, while fibre remains essential but may require a more personalised approach — especially for those starting from a depleted baseline.

The Practical Takeaway

If you care about your long-term health, these are two daily non-negotiables:

Eat a diverse range of prebiotic-rich whole plant foods

Aim for variety in your legumes, whole grains, vegetables, fruits, nuts, seeds, herbs, and spices. The more diversity on your plate, the more diversity in your gut.

Include fermented foods daily

Even a few servings of yoghurt, kefir, kimchi, sauerkraut, or kombucha can make a meaningful difference.

This isn't about perfection. It's about consistently nourishing the 38 trillion microbes that are working around the clock to keep you healthy. Feed them well, and they'll return the favour.