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How to Establish a Healthy Microbiome from Birth
30 September

How to Establish a Healthy Microbiome from Birth

By Cornelia Holten
Published: 30th September 2019
Above image: Julia and Nicholas Holten eating vegetables straight from the garden with millions of beneficial microorganism attached to the roots, leaves and fruits of vegetables.


We are a holobiont, a walking, talking rainforest of more than one species of organisms that form one ecological unity – we call it “human”. Different parts of the body, different ecologies within the body are communicating with one another in order for our body to function.

Studying the microbiome is the hottest area of scientific research within medicine as we are trying to understand just how important the microbiome is.

I will be publishing a few blog posts on the newest scientific research in regard to the microbiome over the next few months and this one will discuss the ways the microbiome gets established in our human body from birth – setting the stage, building the foundation for a great immune system.

We used to think that the female womb and birthing canal are sterile environments, but scientists have found mum’s unique gut bacteria in amniotic fluid and even in the chord blood. So the establishment of a healthy microbiome for the baby starts with the mum and getting her microbiome healthy and balanced should be the priority before even conceiving a child.

We will be discussing ways to foster a healthy microbiome in another blog post, so watch out for it!

The mum provides the foundation for the baby’s microbiome. The breaking of water while giving birth releases the microbes that are sticking to the birth canal. This makes them open for transfer to the baby. As the baby moves through the birth canal he/she is picking up huge amounts of microbes. They stick to the skin, mouth, nose, ears and so on.

An interesting fact is that in the second trimester of pregnancy a particular bacterium called lactobacillus johnsonii starts to become present in high numbers in mum’s vaginal canal. One of its main functions is digesting milk. I can’t remember the last time I drank a glass of milk through the vagina, so the only reason for it to be present there is to inoculate the baby so he/she has the ability to digest milk right away.

If having a cesarean birth you can ask your midwife to do a swab if this is not routinely done in the hospital and you can also have this written up as part of your birthing plan. This is generally done with clean sponges and the baby gets inoculated this way. A little cotton bud can be used to inoculate the gum and mouth with those beneficial, milk-digesting bacteria. The sterile conditions of an operating room is not what a baby needs at birth and studies show that children are more likely to develop food allergies, asthma and eczema later in life when they are born via c-section.

Skin-on-skin contact with mum and dad straight after birth is then the next chapter of the baby’s inoculation journey. Kisses and touching and holding by close family and community members expose the baby to more skin, mouth and gut bacteria.

Then there is breastfeeding. Breast milk provides the greatest nutrition on this planet, but it is not only nutrient-dense, it is also bacterial-dense. Studies show that it contains six to eight hundred different species of bacteria – it is loaded with microbes. Breast milk also contains up to 200 oligosaccharides that are not digestible to the infant. They are prebiotics and feed the microbes that are starting to establish in baby’s gut.

Somehow the breast knows exactly what to give baby to set that gut right, to get that immune system ticking along, and to deliver that nutrition that baby's immature organs and nervous system needs.

Mom's breast knows when to deliver immunoglobulins. They are antibodies produced mainly by plasma cells that are used by the immune system to neutralize pathogens such as pathogenic bacteria and viruses.

From 3 months of age the baby starts to pick up EVERYTHING and direct it to his/her mouth. The baby uses the mouth to inspect objects and to discover the taste and texture. While doing so he/she picks up microbes from the environment.

When the baby is ready for solid food mothers and grandmothers used to simply pre-chew food like broad beans and potatoes and then giving it to the baby with their saliva and millions of beneficial bacteria on it – simple and so effective. Nowadays baby food from the supermarket has been heat-treated and is sterile. The baby misses out on this wonderful inoculation so going back to “old” ways is certainly beneficial for our baby’s well-being. 

The microbiome is not set until children are at least 2 years old. So a lot can be done in those 2 years to set that stage for the future and there is plenty of time to remedy a traumatic birth for example or if there was a need for antibiotics early on.

Time spent outdoors on a spray-free lawn without “protective” mat, in a vegetable garden or an organic agricultural field is the best you can give your child – billions of beneficial bacteria per teaspoon of healthy soil!

As humans we cannot exist or thrive on isolations. We are what we are because of our ability to pick up organisms from the environment and creating the holobiont.

I hope you enjoyed this article and learnt a thing or two. In the next article I will be discussing healthy soil and the importance of regional food for our microbiome.

See you next time.



About Cornelia Holten

Cornelia Holten

Cornelia is an herbalist and slow food educator with a passion for simple living, DIY, herbs and self-sufficiency. A certificate in Organic Horticulture, the Soil Food Web, an Apprenticeship in Herbal Medicine and living on a farm in Pigeon Bay equip her with a lot of knowledge and experience with growing food and living a healthy life.

She is teaching workshops on sustainable food systems, whole foods, fermentation, primal diets and organic gardening. A thirst for knowledge and a passion for new scientific studies keep her well informed on those topics.