The impact of processed foods on the gut microbiome

In the 1990s, a Brazilian scientist named Carolos Monteiro noticed that childhood obesity rates were climbing fast in Brazil.¹ But looking deeper into the matter, he noticed that it wasn’t just about the children eating too much salt and sugar. Instead, they realised that the bigger change was in what people were eating, and not just how much.¹

Households were moving away from traditional staples like rice, beans, and fresh produce and replacing them with processed products like fizzy drinks, packaged breads, sausages, instant noodles, and sweets. These foods were not only calorie-dense, but were fundamentally different from real, whole foods. Monteiro coined a new term for them: ultra-processed foods, or UPFs.¹ And ever since, research has been stacking up linking UPFs to a long list of health problems, from heart disease and diabetes to gastrointestinal issues and even depression.

What are ultraprocessed foods?

First off, not all forms of processing are bad. For instance, freezing peas or pasteurising milk is still considered processing, but it doesn’t destroy the food’s basic nature. Ultraproceed foods are different.² They’re industrial products built largely from cheap ingredients you wouldn’t recognise in your own home; things like high-fructose corn syrup, soy protein isolates, emulsifiers, and artificial flavourings.³

If a food’s ingredient list reads like your KS3 science experiment, it’s most likely a UPF. Think fizzy drinks, certain cereals, processed meats, microwave meals - basically, anything far removed from its natural state. Although these foods are everywhere, that doesn’t mean you should always opt for them.

How UPFs harm your health

Research has consistently shown that diets high in UPFs are linked to a multitude of health issues, including obesity, type 2 diabetes, heart disease, bowel diseases, and mental health conditions.²

It’s easy to see how certain processed foods can contribute to weight gain, given they’re very palatable, packed with sugar and fat, and easy to overindulge in. However, scientists believe that UPFs do more than just pack a calorific punch. They may be actively changing some ways your body functions, starting with your gut.²

Meet your microbiome

Your gut microbiome is a vibrant community of trillions of bacteria, viruses, and fungi living in your intestines. These tiny organisms help you digest food, regulate your immune system, produce essential nutrients, and even influence your mood. A healthy, diverse microbiome is linked to lower rates of chronic disease, better mental health, stronger immune defenses, and a longer lifespan. But disrupt this ecosystem, and things can go south fast.⁴

Gut microbiome imbalances, known as dysbiosis, are associated with everything from obesity and diabetes to autoimmune conditions and anxiety.^2-4 And that’s where UPFs come into play. According to research, UPFs:⁵

• Reduce the diversity of your microbiome, meaning fewer beneficial bacteria thrive.

• Weaken the gut barrier, leading to “leaky gut” which is where harmful substances can pass into the bloodstream and trigger inflammation.

• Promote the growth of harmful bacteria, some of which are linked to health conditions.

• Starve beneficial bacteria out of the fibre they need to survive.

The gut microbiome can respond to dietary changes in as little as a few days.^4,5 That means every meal you eat has the potential to either feed and support your good bacteria, or push your gut further into dysfunction.

A little about the additives

Part of the damage from UPFs may come from the food additives they contain. Ingredients like emulsifiers (which keep foods smooth and creamy) and artificial sweeteners (which replace sugar) have been shown in animal and human studies to disrupt the gut microbiome and promote inflammation.⁵

For example, emulsifiers like carboxymethylcellulose and polysorbate-80 have been linked to changes in gut bacteria that lead to intestinal inflammation and metabolic disorders in mice.⁶ Some artificial sweeteners may also negatively affect gut bacteria, impairing blood sugar control.⁵

Can the damage be undone?

Despite being susceptible to damage by a microwave meal, your microbiome is able to recover over time. With dietary changes, you can start healing your gut and shifting your bacterial populations in a healthier direction.

Here are some simple steps to protect your microbiome:⁷

• Eat more fibre-rich foods: Fruits, vegetables, legumes, nuts, seeds, and whole grains feed your good gut bacteria.

• Limit ultraprocessed foods: Focus on cutting back on sugary drinks, packaged snacks, and fast food.

• Cook more at home: Preparing meals from scratch helps you control ingredients and minimise additives.

• Choose minimally processed options: Swap plain yoghurt for flavoured ones, or fresh bakery bread for packaged loaves.

• Focus on diversity: A variety of plant-based foods can nourish a wider range of beneficial bacteria.

• Stay hydrated: Water helps keep digestion running smoothly and supports gut health.

The numan take

While ultraprocessed foods have become a staple in the modern-day Western diet, it doesn’t mean we can’t shift back to consuming fresh, whole foods more often. By making small, consistent changes in your diet and focusing more on cooking, you can start to improve your gut health.

References

1. ^{Humphreys G. Carlos Augusto Monteiro: nutrition and obesity. Bulletin of the World Health Organization. 2024;102(8): 560–561.}

2. ^{Brichacek AL, Florkowski M, Abiona E, Frank KM. Ultra-processed foods: A narrative review of the impact on the human gut microbiome and variations in classification methods. Nutrients. 2024;16(11): 1738.}

3. ^{Monteiro CA, Cannon G, Levy RB, Moubarac JC, Louzada ML, Rauber F, et al. Ultra-processed foods: what they are and how to identify them. Public health nutrition. 2019;22(5): 936–941.}

4. ^{Ghosh TS, Shanahan F, O’Toole PW. The gut microbiome as a modulator of healthy ageing. Nature reviews. Gastroenterology & hepatology. 2022;19(9): 565–584.}

5. ^{Whelan K, Bancil AS, Lindsay JO, Chassaing B. Ultra-processed foods and food additives in gut health and disease. Nature reviews. Gastroenterology & hepatology. 2024;21(6): 406–427.}

6. ^{Panyod S, Wu WK, Chang CT, Wada N, Ho HC, Lo YL, et al. Common dietary emulsifiers promote metabolic disorders and intestinal microbiota dysbiosis in mice. Communications biology. 2024;7(1): 749.}

7. ^{Aziz T, Hussain N, Hameed Z, Lin L. Elucidating the role of diet in maintaining gut health to reduce the risk of obesity, cardiovascular and other age-related inflammatory diseases: recent challenges and future recommendations. Gut microbes. 2024;16(1): 2297864.}