How diet shapes your gut microbiome
The gut microbiome is a diverse community of trillions of bacteria, fungi, and other microbes that flourishes on what we eat. Each dietary pattern – omnivorous, vegetarian, or vegan – nurtures a unique microbial ‘garden’ that affects health in many ways.
The microbiome and diet
Currently, there are a host of different labels for diets. Vegan, pescatarian, flexitarian you name it. In a study published in Nature Microbiology, the microbiome of 21,561 people on vegan, vegetarian and omnivore diets was compared. This study found that people who ate more plant-based foods had more bacteria that was linked to better heart and cardiometabolic health.
This same microbiome study showed that a plant-based diet generally supports a more diverse gut microbiome linked with better overall health. However, it’s not just about eliminating animal products: omnivores can boost their microbiome by adding more plant foods to their plate. Fibre is the main key to these types of diets. Plant-based foods like legumes, whole grains, and vegetables contain prebiotics which are fuel for good bacteria. This makes a vegetarian or vegan diet especially microbiome-friendly.
Plants also contain polyphenols which are natural compounds known for their antioxidant properties which have numerous benefits for health and disease prevention. What’s great about polyphenols is that there are different types in different colours of vegetables all with unique health benefits so it’s important to eat a variety of vegetables.
However, diets high in ultra-processed foods, high in red meat or low in fibre can harm the gut microbiome, which may lead to inflammation, weight gain, and poor cardiometabolic health. Limiting ultra-processed foods and red meat benefits everyone, regardless of diet patterns.
Top three tips for a healthier gut microbiome
1. Eat more plants
Include fruits, vegetables, legumes, and whole grains in every meal
2. Avoid processed foods
Minimise added sugar, artificial additives, and unhealthy fats
3. Diversify your diet
Try new plant-based foods to support a variety of gut bacteria
The downside of a diet high in animal products
Diets high in animal products, such as red meat and eggs, contribute to an increase in the fermentation of protein in the gut which can lead to disruption of the protective gut lining, less production of short-chain fatty acids (SCFA) and higher trimethylamine N-oxide (TMAO) levels. High levels of TMAO in your blood can increase the risk of heart disease. It is produced when bacteria in your gut break down certain nutrients like choline and l-carnitine, which are higher in meat products and turn them into a substance called trimethylamine (TMA). TMA then goes to your liver, where it's changed into TMAO.
Not all plant-based diets are great though, plant-based diets, high in refined grains, sugary beverages, processed and fried foods, can decrease microbial diversity and foster the growth of unhealthy species of gut bacteria. Such diets are linked to higher levels of inflammation and a higher risk of chronic diseases, reversing the potential benefits of plant-based eating.
This advice doesn’t mean all plant-based foods are equal, less processed, whole foods are the way to go. A 2024 study of 705 adults published in The American Journal of Clinical Nutrition those following a healthy plant-based diet had greater gut microbial diversity and lower TMAO levels than those adhering to an unhealthy plant-based diet. These findings highlight the need for mindful food choices, even within plant-based eating, and that reducing processed foods and added sugars is essential to avoid this microbiome imbalance.
Where to from here?
Not all plant-based diets are equal, so ensure there’s a wide variety of plant-based foods in your diet, and limit ultra-processed foods and red meat. There’s hope for omnivores out there who eat plenty of diverse plant-based foods as this can increase the beneficial microbes in their gut to levels like those of vegetarians or vegans.