Your Baby’s Microbiome: Setting the foundations for a healthy future

Chloe breastfeeding her baby Skin-to-skin shortly after birth

What is the microbiome?

Your microbiome is the diverse community of microorganisms (bacteria, viruses, fungi ect) which live within your body. These microbes are vital to our existence. They aid digestion, produce vitamins and neurochemicals, interact with our hormones, and protect us from infection. In return we give them an ideal place to live. We couldn’t live without them, and they couldn’t live without us. As adults, we actually have between 10 and 100 times more microbes than human cells in our bodies, and inhale around 860,000 bacteria per day!

How does a baby’s microbiome develop?

At birth

In utero, our babies grow in a *near* sterile environment. They are a clean slate, yet to be colonised with their own microbiome. During the last trimester of pregnancy, there is a change in the microbe population inside a mother’s vagina and intestines. The diversity of the microbe population decreases, and the number of Lactobacilli bacteria drastically increase. These Lactobacilli bacteria help us to break down lactose (the main sugar in breastmilk) as well as other sugars, so that we can extract more energy from them. During a vaginal birth (and potentially during a surgical birth, too) baby is exposed to the microbe population in the mother’s vagina, and potentially those in her intestines too. These microbes coat baby’s skin, mouth and nose, make their way to baby’s gut, and begin to form the foundations of baby’s own microbiome.

Skin-to-skin contact

Ideally, baby is placed skin-to-skin with their mother immediately after birth. The population of microbes which live on our skin is as individual as our fingerprints, determined by our own birth, our environment, our diet, our medical history, and lots of other things in between. When a baby is placed directly onto their mother’s skin, this allows the mother’s skin microbes to colonise her baby’s skin. These friendly bacteria and fungi help to prevent pathogens (disease-causing microbes) finding a home on baby’s skin, by taking up all the room and giving off anti-microbial substances. Skin-to-skin contact continues to benefit your baby throughout the first weeks, months, and years of their life, so even if you are unable to have immediate skin-to-skin contact with your baby, they can still reap the benefits at a later date.

Immediate skin-to-skin after birth carries amazing benefits for your baby


Your breastmilk is incredible. It provides your baby with a perfect balance of nutrients and hundreds of non-nutritive compounds which help them to grow and protect them from infection.

As discussed above, during birth some of the first bacteria to populate your baby’s body are Lactobacilli bacteria, which help your baby to digest the sugars in your milk and absorb as much energy from it as possible.

Your breastmilk also contains its own community of microorganisms. Every time your baby feeds, you pass them hundreds of different species of friendly microorganisms which, just like the microbiome of your skin and vagina, defend your baby against infection and help them to digest their milk. In addition to this, your baby passes YOU some of the microorganisms living in their mouth, nose and on their skin. These microorganisms join the microbiome in your milk. If any pathogens are present, your body recognises these and initiates an immune response, producing antibodies to give to your baby at the next feed.

Breastmilk also contains special types of indigestible sugars: Human Milk Oligosaccharides (HMO). These sugars are prebiotics. Your baby can’t digest them, but their microbiome can! These HMOs feed the friendly bacteria in your baby’s gut, selectively nourishing your baby’s microbiome and allowing it to flourish, and this community of microorganisms train your baby’s immune system. It really is amazing stuff!

How does this affect baby’s future health?

Having a healthy microbiome during those first few months of life trains your baby’s immune system and helps to protect them against infection. A baby’s immune system is underdeveloped at birth, and is suppressed during the final weeks of pregnancy to allow baby to be colonised with mum’s microorganisms during birth and breastfeeding. These ‘good’ microbes help baby’s immune system to recognise and fight the ‘bad’ microbes, and this lasts throughout their entire life.

Emerging research shows that, as well as protecting your baby from infection and aiding digestion, having a healthy microbiome also protects them from Non-Communicable Diseases in later life, such as diabetes, asthma, cancer, digestive disorders, and even mental illness.

This is a fascinating new area of research, and there is still lots we have to learn. The latest science suggests that allowing a baby to develop a healthy microbiome during birth and breastfeeding sets the foundations for a healthy future, and that interrupting the natural sequence of colonisation can have life-long consequences for our children, and their children, and so on. Our microbiome is an organ in its own right, and one which is vital to our health. We need to take good care of it!

Learn more here:


The Microbiome Effect- Toni Harman & Alex Wakeford

UNICEF Emerging Research: Epigenetics and the Microbiome

World Health Organisation: The Infant Microbiome

Protima Amon, Ian Sanderson, What is the Microbiome?, British Medical Journal

The information on this page should not be used in place of medical advice. Information found online should always be discussed with your own IBCLC, Dr or Midwife to ensure it is appropriate for you and your baby’s situation. Contact your Dr, Midwife or Health Visitor with any concerns about your own or your baby’s health and welfare.

Disclaimer: The views, thoughts, and opinions expressed in the text on all pages of this website belong solely to the author, and do not necessarily reflect the views of the author’s employer, organization, committee or any other group or individual, unless explicitly stated otherwise.

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