How can we support our microbiome?

There are many ways to support and maintain a healthy microbiome.

It all starts at the very beginning.

We and our microbes have developed a beautiful interplay over the last million years. During birth, we pass through our mother’s birth canal, which is teeming with Lactobacilli. Our skin and mouth soak up the bacteria like a sponge. When drinking from the breast, we take in the colostrum, which washes down the Lactobacilli with their favourite nutrient: milk sugars.

This allows the Lactobacilli to be the first bacteria to settle in our gut, supporting our digestion of the milk that nurses us over the next several months. The mother's breastmilk furthermore contains special sugars that enable the next “originator species” to settle, Bifidobacterium infantis. This natural way of birth and breastfeeding has existed for millions of years and selects the “good guys” to establish themselves in our gut and to banish the “bad guys”.

If the normal passage through the birth canal is replaced by a caesarean section, the exposure to Lactobacilli will be missing and the healthy colonization of our gut will be in part delayed. At the moment, we don't know the precise ways in which this delayed population of our healthy gut microbiome influences our development. You are surely doing something good for your baby if you give him or her a natural birth and breastfeed, if it is possible for you.

An apple a day keeps the doctor away

High fiber foods

Before we enter the area of nutrition it is important to us to make the following statement: Our microbiome and its interactions with our body are highly complex and we are just beginning to understand tiny fractions of it.

MyMicrobiome is not giving any advice on what you should eat or not eat. We only present the various scientific theories that you, our welcomed reader, can form your own opinion on.

With our diet we decide which bacteria we cultivate and which we do not. If you eat a variety of foods, there will be a greater diversity of bacteria in your gut. Your gut bacteria love dietary fiber from foods like fruits, vegetables, nuts, legumes and whole grains. When digesting fiber, bacteria produce short chain fatty acids that nourish the gut barrier, improve immunity function and prevent inflammation, which reduces the risk of cancer.

And here's very good news …

Coffee, Tea and Chocolate

… apart from fruits and vegetables, even tea, coffee, wine and dark chocolate have correlated with an increased diversity of our gut microbiome. These foods contain polyphenols, which are naturally-occurring antioxidant compounds. Also, yoghurt delivers helpful bacteria to your gut.

On the other hand, foods which are rich in dietary fat and simple sugars are correlated with a decreased diversity of our gut microbiome.

As well the way food is prepared matters. Fresh, raw food contains more fiber than processed food, such as fried food.

Food can also be a vehicle for introducing good bacteria into your gut. Fermented foods, for example, are full of beneficial bacteria such as Lactobacillus or Bifidobacterium. To put it into a nutshell, the smaller the variety of the food you eat, the slimmer the diversity of your microbiome.

Are you a tidy person?

Society has developed perfectly sophisticated hygiene methods in an effort to move towards a more and more sterile environment. The cost of this obsession with hygiene range from allergies to asthma. During our daily shower routine, using detergents to rub off our commensals from every square centimetre, our  skin has a hard time staying in balance and becomes either too dry or too oily. In turn we suffer from dandruff and pimples or even acne.

Microbiome scientists were curious just how much diversity we’ve already lost and so they analysed the fecal, oral and skin microbiome of an isolated Yanomami Amerindian village.

Besides their fecal microbiome, their skin microbiome was completely different from U.S. subjects with a much higher diversity. While the skin microbiome of the western civilisation is dominated by Staphylococci, no single bacterial group dominated the skin microbiome of the Yanomami. Even bacteria which were previously reported as soil bacteria, were enriched in their skin microbiota. This may easily be explained: they live closer to nature and wear fewer clothes in contrast to us, who spend most of our lives inside, washing away the dirt after we were outside …

In short, our skin microbiome benefits if we spend more time outside, let our kids play in the dirt and maybe even join them!

Be careful when choosing your daily hygiene products such as anti-bacterial soap or disinfectants. Have a closer look at the ingredients of your antiperspirant, toothpaste, mouthwash and facial cleansing products. All these products can potentially harm your skin's microbiome. In this case, less is more, which means using less products with fewer ingredients less frequently will give your microbiome time to recover. Ideally, "Microbiome-friendly" certified products should be used.


Last but not least, a major impact on our body's microbiome is caused by antibiotics (more about: antibiotics and the microbiome)

Antibiotics do not only reduce bacteria that cause infection but also our commensal bacteria and, if taken orally, are effective in our whole body, not only at the site of infection. Before taking them, keep in mind it will come with side effects and it can take months or even years until your microbial ecosystems recover. On top,  due to the disturbed microbiome the immune system is also weakened and thus more susceptible to the next infection.

So think twice before taking an antibiotic. Talk to your physician about your infection – ideally an analysis of the infectious agent would help to specify the antibiotic to be taken. In case of a virus infection, antibiotics are not effective.


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– The independent certification and research institute for our microbiome –

DISCLAIMER: Nothing on this site or blog is intended to provide medical advice, diagnosis or treatment.


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