How Clean is Too Clean?

The role of the microbiome in your baby's life

Did you know our bodies are populated by billions of microscopic organisms (microbes)? In our digestive tract, respiratory and reproductive systems, and all over our skin? Don't worry – they naturally form what's called the human microbiome, an essential part of our development and lifelong health. To help support the development of your baby's gut microbiome it is important to understand what a ‘microbiome' is, the role it plays in their life, and why creating an environment that exposes them to a range of microbes is actually a good thing.

What is the microbiome?

It's the world's most important ecosystem. A complex collection of bacteria, viruses and fungi associated with the human body, and found naturally on the skin, in the mouth, lungs and gut. Together, these microbes break down food, help make vitamins, keep your skin healthy, and most importantly, work with your immune system to fight off infections and disease.

It's now thought that the changes in our intestine's microbiome influence a range of modern diseases and disorders like inflammatory bowel disease (IBD), allergy, diabetes, and obesity. Though scientists are only starting to understand the microbiome's complex role in our lives, it's clear just how much it influences our health.

And that's why building a healthy one for your baby is so vital.

The important years

Your baby's immune system is created hand-in-hand with their microbiome, and is nearly fully developed by 3-5 years of age. This process has lifelong health consequences, and may affect their metabolic, physiological, immunological and neurological growth.

Every microbiome is unique. Just think of it as your baby's bacterial thumbprint, influenced by a range of factors such as the environment they grow up in, the foods they eat, cultural traditions, delivery method, antibiotic treatment, genetics and so on.

For example, when you breastfeed your baby, you're actually giving them part of your own microbiome. This plays a key role in building a healthy immune system, as well as protecting them against diarrhoea, respiratory disease, and obesity. And while the effects aren't fully understood, scientists have found differences in microbiomes between babies who've been delivered vaginally or through caesarean.

What's not surprising is that your baby's gut microbiome changes once solid foods are introduced (at 4 to 6 months). So it's clear that what they eat may impact their health for years to come.

Loosen up on the cleaning front

We're a society obsessed with cleanliness. You might think this is a good thing, but it could be making our microbiomes weaker, causing the gut microbiome of each generation to have less microbial diversity.

So our message to parents is – loosen up on the cleaning front. Of course, we know it's important to protect your children from nasty pathogens and viruses, and to teach them good hygiene practices like washing their hands after going to the toilet. But if you can encourage your kids to play outside, crawl around on the grass, and get a little dirty – then their immune systems will thank us. Not just now, but for years to come.

Other ways to help foster your baby's gut microbiome is by using antibiotics only when necessary, feeding them a range of good foods, finding animals for them to pet, and avoiding antibacterial soaps.

Summing it up

  • What: The microbiome is the complex collection of bacteria, viruses and fungi associated with the human body, found naturally on our skin, mouth, lungs and most importantly, our gut. Together they break down food, make vitamins, keep your skin healthy, and develop our immune system.
  • When: Your baby's microbiome develops hand-in-hand with their immune system, from conception to around 3 to 5 years of age. These first few years are crucial when it comes to shaping their health and development.
  • How: Though your baby's microbiome is naturally formed, there are ways you can help strengthen it. Everything from breastfeeding and avoiding antibiotics when possible, to encouraging them to play outside and put things in their mouth. Remember, getting a little dirty is healthy for them.
  • Who: Every baby's gut microbiome is different, and is influenced by a range of factors such as genetics, exposure to different environments, first foods, cultural traditions, delivery method, antibiotic use, and more.
  • Why: The healthier your baby's microbiome, the more robust their immune system will be. This makes it easier for them to fight off diseases and infections and less likely that they will develop disorders such as inflammatory bowel disease, allergy, diabetes and obesity.

How to help shape your baby's microbiome

  1. Stay close – from the moment your baby is born, they need healthy bacteria. Things like skin-to-skin contact and breastfeeding can ensure this. (see Communication with your baby; Understanding attachment and bonding)
  2. Get dirty – as mentioned above, there's nothing wrong with getting a little dirty. So don't worry about the mud on their feet or the dirt under their nails. Encourage lots of playing outside. It's good for them. Every now and then take them to a petting zoo, or let them play with your neighbour's dog. And try not to go overboard on the laundry and disinfecting fronts. (see Understanding the importance of play; Physical activity in young children)
  3. Cut the junk – getting rid of sugary or processed foods from your baby's diet helps strengthen their microbiome and build their immune system. So cut down on the chips and lollies.
  4. Feed them foods which contain prebiotics and/or probiotics – yoghurt, miso and sauerkraut contain natural probiotics which are believed to benefit the gut microbiome, while onions, garlic, cabbage and high-fibre foods like asparagus, bananas and beans, contain prebiotics which are all thought to help shape the immune and digestive systems.
  5. Listen to your doctor – sometimes the ‘dirt is good' mantra might not apply to your baby, especially if they were born prematurely or if they're immunocompromised. So always follow the advice of your doctor when it comes to hygiene and infection control.

Some more insight

If you're pregnant and interested in learning more about the human microbiome, you might like to watch Microbirth, a documentary about how microscopic events during childbirth have lifelong consequences for the health of our children. It won the Grand Prix Award at 2014 Life Sciences Film Festival in 2014. You can watch the trailer and purchase a copy at