Good for you, good for your microbes!

By Elisa Di Stefano, PhD

We all know the importance of a healthy diet for our well-being. But do you know that when you eat, you are also feeding trillions of tiny microbes that inhabit your gut?

The collection of these microbes is called your gut microbiota. It is in fact unique to each person and develops over a lifetime.

Diet is a big player in shaping the composition of the gut microbiota, as the type of food we eat determines the type of food components that are not digested and reach the colon. These undigested food components are food for the gut microbes, which produce metabolites that in turn contribute to our wellbeing. Each microbe has its own preference for certain food components over others. So, what food should we choose to keep our microbes happy?

 A review from APC Microbiome Ireland recently addressed this question and looked at which foods can help or harm our own gut microbiome. 

Defining healthy eating

Before classifying specific foods as healthy for the microbes, we must first define what healthy eating means in general. 

With dietary guidelines, countries intend to encourage eating and lifestyle habits which allow sufficient nutrients supply while preventing chronic diseases.

Despite country-to-country variations, there is strong consistency in the core elements of healthy eating: abundance of whole grains, fruit and vegetables complemented by moderate amounts of animal or plant-based protein sources, and avoidance of sugar/salt/saturated fat rich foods.

Now that we have defined healthy eating, let’s look at specific foods and their impact on the health of our gut microbes.

The good ones:

Whole-plant foods like fruits, vegetables, whole grains, legumes, nuts. These are the golden foods for our gut microbes, as they are the only relevant natural source of dietary fibers. Fibers are indigestible carbohydrates that reach the colon intact, where they are fermented by gut bacteria to tiny molecules called short-chain fatty acids (SCFAs), which have a wide range of health benefits for the human host.

Another key component of whole-plant foods are phytochemicals. These molecules provide color, flavor and astringency to plants. Similarly to fibers, they mainly go through our digestive system untouched. In the colon, many phytochemicals are rearranged in a new chemical structure (or “biotransformed”) by gut microbes.

The resulting molecules can easily be absorbed by our body at this stage, having terrific activities as antioxidants and modulators of the immune system.   

Note: choose your grains wisely. It is the bran layer of whole grains that contains the precious phytochemicals and dietary fibers! This is usually removed in refined grains and flours.

Fatty fish. Packed with the cardioprotective omega-3 fatty acids eicosapentanoic acid (EPA) and docosahexanoic acid (DHA), fatty fish seem to also promote growth of specific beneficial gut microbes. In turn, the metabolism of omega-3 fatty acids by gut microbes could mediate their health benefits, but more research is needed to draw conclusions.

The controversial ones:

Red meat. Meat contains essential micronutrients and high-quality proteins. However, fermentation of such proteins by gut microbes releases metabolites that, in tandem with other red meat components like heme, activate a cascade of reactions leading to increased carcinogenic potential.

L-carnitine and phosphatidycholine, another two compounds abundant in red meat, are converted by gut microbes into molecule trimethylamine-N-oxide (TMAO), which is strongly implicated in cardiovascular disease (CVD). Interestingly, TMAO is also highly abundant in fatty fish, where consumption can instead counteract CVD, leaving questions open on the impact of TMAO specifically.

Dairy products. As a main source of calcium, phosphorus, and vitamin D when fortified, dietary guidelines tend to find space for a limited consumption of dairy products. Nevertheless, we can’t ignore that their abundant saturated fats can be converted by gut microbes to detrimental metabolites. Future well-designed human trials will hopefully tell us the verdict.  

The bad ones:

Ultra-processed foods. These are industrial food products made almost entirely by ingredients previously extracted from foods or synthesized, from the salty industrial frozen pizza to packaged bread.

Bread? Artisanal or not, bread is bread, right?

If you could ask your gut microbes, they would certainly say “No!” 

While different qualities of bread could appear similar at a first sight, there is a fundamental difference. As a result of being made by purified ingredients, ultra-processed foods lack the three-dimensional structures present in plant cells, which means they are higher energy density products with acellular nutrients that are much easier to digest and absorb for our body. This can cause overgrowth of bacteria in the small intestine,leaving little food left for the colon. Further, certain food additives characteristic of ultra-processed foods alter gut homeostasis, and the high salt content decreases the abundance of beneficial gut microbes such as Lactobacilli, both promoting gut inflammation and impairing health. 

Processed meats. Adding to the controversial metabolites generated by gut microbes’ fermentation of red meat, the high content of saturated fats and curing agents like nitrate and nitrite in processed meats are implicated in the formation of carcinogenic compounds through gut microbes metabolism. We are left with no options but to disqualify these products for gut health.  

Concluding thoughts

Now, knowing that our diet strongly shapes our gut microbiome, there are a few dietary habits to follow if we want to make the good gut microbes happy: (1) eat tons of fruit, vegetables and whole grains; (2) include food sources with sufficient omega-3 fatty acids; (3) moderate consumption of meat and dairy; (4) avoid ultra-processed foods.

This said, exciting opportunities in reformulation of processed foods could facilitate a daily inclusion of microbiome-approved foods, without challenging consumers in modifying their eating habits. To the food industry and to the informed consumer the power to choose wisely!

Peer-edited by Gabrielle Dardis, PhD Candidate in Biochemistry and Biophysics

Picture credit: Sarema/

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