How can we support our microbiome?

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

It all starts at the very beginning
It all starts at the very beginning

It all starts at the very beginning

We and our microbes have developed a beautiful interplay over the last million years. During birth, we passed through our mother’s birth canal, which is teeming with Lactobacilli. Our skin and mouth soaked up the bacteria like a sponge. The next thing we did was to breastfeed, taking in the colostrum which washed down the Lactobacilli with their favourite nutrient: milk sugars.

This allowed the Lactobacilli to be the first bacteria to settle in our gut, supporting our digestion of the milk that would nurse 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, but you are surely doing something good for your baby if you allow him or her a natural birth and breastfeed, if possible.

An apple a day keeps the doctor away

High fibre foods
Your gut bacteria love dietary fibre from foods like fruits, vegetables, nuts, legumes and whole grains

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 …

… 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.

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

Also, 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. This kind of food is called probiotic.
Fermented foods, for example, are full of beneficial bacteria such as Lactobacillus or Bifidobacterium.

To put it into simpler terms, the more you restrict the variety of food that you eat, the slimmer the diversity of your microbiome is going to be.

Also, yoghurt delivers helpful bacteria to your gut.

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 of our skin results we lost a big part of our microbial diversity. Our skin has a hard time staying in balance, and it becomes either too dry or too oily, and we in turn 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 would benefit if we spent more time outside, letting our kids play in the dirt and maybe even joining 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. There´s no need to kill your commensal bacteria. Washing your hands with normal soap is more than enough, no disinfectant needed!

You may even want to try this one: Mother Dirt. The company AOBiome wants you to ditch the soap and wash with bacteria instead! A New York Times Magazine journalist replaced her traditional cleansing products with the bacteria treatment and experienced a softer and smoother skin than ever before!

The company AOBiome wants you to ditch the soap
The company AOBiome wants you to ditch the soap and wash with bacteria instead!
Zendium products promotes the growth of good bacteria in my mouth


I just recently saw an advertisement for a toothpaste that promotes the growth of good bacteria in my mouth. Maybe I'll try it and let you know if it works!


Last but not least, the worst enemy of our microbiome: antibiotics (more about: antibiotics)

Before taking them, keep in mind you are throwing an atomic bomb at your microbial ecosystems. It will take years until they recover, if at all. But not only that, your system is also weakened and thus more susceptible to the next infection.

So think twice before taking an antibiotic: are you really feeling that bad, or can you wait a few more days? Talk to your physician about your infection – maybe it was even caused by a virus, which makes the use of an antibiotic senseless.


If you are curious about your microbiome and want to read more, I highly recommend this book by Prof. Martin J. Blaser, director of the NYU Human Microbiome Program.

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