Food the Microbiome Loves

assorted vegetables on crates
Photo by Min An on

Who doesn’t like to shop at the farmers market? Fresh produce picked that morning or the day before. It doesn’t get any better, doesn’t it? You can talk to farmer and ask if they grow organically even though they are not actually licensed. Many farmers will tell you that they don’t spray their crops. Of course you will find vegetables with blemishes. That only can happen when the farmer doesn’t use any chemicals.

We find foods we love but we can choose from a wide variety of vegetables and proteins that our gut microbiome loves as well.

But lets talk about how you can help your microbiome to thrive.

We have many different beneficial bacteria in our gut and we want to keep them happy with the food they love.

Different gut bacteria thrive on different foods. It’s that simple. Bacteria consume fibers and the different foods contain different fibers.

It’s also important to find organic produce if possible since they will at least contain less chemicals and they contain more nutrients.

The commensal bacteria, which are the beneficial kind, like to eat fibers, polyphenols & antioxidants

Which foods are high in Fiber, Polyphenols & Antioxidants

assorted nuts lot
Photo by Dmitry Zvolskiy on
  • Fruits
  • Vegetables
  • Legumes
  • Whole Grains
  • Nuts & Seeds
  • Herbs & Spices

Protein & fats are very important as well. Grass fed beef, free ranched chicken and their eggs. Butter, Lard and Olive oil are healthy fats.

Saturated fat, sugar and processed foods are not helpful to the microbiome but the pathogens in the gut love those.

Alcohol when consumed on a regular basis contributes to dysbiosis in the gut microbiome.

For everyone who uses guar gum or other emulsifiers when they bake with gluten free flours need to know that those products can have a negative impact on the mucosal barrier when consumed in larger amounts. A tiny teaspoon in 1 cup of flour is not a lot and you will not eat the whole cake you bake or the plate of cookies all at once. So, don’t drive yourself crazy. You know if you can tolerate those emulsifiers or not. Maybe switching to a different one or using a different recipe will do the trick to stay away from those. Remember, you are in charge and nobody else.

Fermented foods like sauerkraut, kimchi, yogurt and kefir contain Lactic Acid bacteria which optimize the pH in the gut.

kimchi in a ceramic bowl

Raw foods are healthy because the nutrients are not destroyed by the cooking process. On the other hand they can cause pathogens to grow and inflammation in the gut. Someone who has gut issues already or is immuno-compromised should look into this subject to protect themselves.

Nowadays we don’t eat many different foods anymore compared to our ancestors.

To find out if this statement is true you could make a list each day for a week of all the foods your consumed. Include all vegetables, fats, proteins, herbs and spices. When you find out that you eat the same foods over and over again then you can add some you hardly ever eat or you never eat. To introduce new foods or a wider variety of different foods ensures that you eat many different fibers which feed the microbiome and you can increase the number of species in your gut

This statement

Diversity in diet = Diversity in Microbiome

is key to understand that eating a lot of different foods is beneficial for the gut microbiome.


are found in fruits, vegetables, cereals, tea, coffee and wine

they are anti-

  inflammatory, oxidant, carcinogenic, adipogenic, diabetic, and


About 5 – 10% of Polyphenols are absorbed in the small intestine while the rest 90 – 95% move to the large intestine and used there by the microbes.

In the large intestine the gut bacteria, Bifidobacteria, Lactobacilli, Akkermansia are supported by polyphenols. At the same time polyphenols act as an antimicrobial to pathogens like Clostridia and Salmonella.

Plant Protein & Animal Protein

If a person increases their consumption of plant based protein the number of Bifidobacteria and Lactobacillus when up and therefor the production of Short-chain-fatty-acids increased in the gut and the gut barrier is strengthened. At the same time inflammation decreased 2

With a diet that was higher in animal protein a decrease in short-chain-fatty acid production due to a decrease in Bifidobacteria was observed.

Fats your Microbiome Loves

The consumption of unsaturated fats from Olive oil or Avocado oil increased lactic acid bacteria like bifidobacteria.

On the other hand a diet high in saturated fats from palm oil or coconut oil showed more of an inflammatory process.

Microbiome Health can be Restored

  1. Diet, & Prebiotics
  2. Digestion
  3. Remove Dysbiosis Risk Factors
  4. Support Commensal gut bacteria
  5. Reduce Inflammation & Rebuild Barriers

  • Reference:
  • 1 Gibson GR, Hutkins R, Sanders ME, Prescot SL, Reimer RA,   Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus 10.1038/nrgastro.2017.75. Epub 2017 Jun 14. PMID: 2861148
  • 2. Singh RK, Chang HW Influence of diet on the gut microbiome and implications for human health. J Transl Med. 2017 Apr 8;15(1):73 doi: 10.1136/gutjnl-2014-307142 PMID: 26900906; PMCID: PMC4856456