Meagan Scott from the Gut Healing Community shares her wisdom with us on how to give babies the best start with a healthy gut

A baby’s gut is home to trillions of bacteria known as the microbiome. Good gut health plays a key role in every aspect of a child’s health & wellbeing and sets them up for a healthy adult life.

Beginning at birth, the gut microbiome performs important duties like breaking down and absorbing food, protecting the gut from harmful bacteria and helping to train a developing immune system to defend the body from infections and illness.

In the first few years of life many factors impact the gut health of a baby.

Firstly, lets discuss these factors in more detail and then look at ways that you can boost a baby’s gut health.

The 5 main key areas that impact the gut health of a baby are:

  1. Mother’s gut health before during and after pregnancy.
  2. Delivery Method.
  3. Antibiotic Use.
  4. Feeding Method.
  5. Diet.


woman pregnant

  1. Mother’s gut health before, during and after pregnancy

At birth, it was always thought that a babies gut was sterile. Samples of umbilical cord blood and babies’ first bowel movements, show that babies already have some gut bacteria, acquired from the mother’s digestive system during pregnancy. As a mother, ensuring a healthy gut flora and looking after your own gut health is important in helping the gut flora of your unborn child before, during and after pregnancy. You can take care of your gut by eating healthy wholefoods, preferably organic or spray-free, avoiding toxins in beauty and cleaning products and staying fit and healthy.

woman giving birth newborn

  1. Delivery Method

Studies have found that the delivery method of a baby, impacts their gut microbiome. During vaginal delivery, babies are exposed to the mother’s flora in the vaginal canal. Whereas babies born via c-section harbor characteristics of the skin flora.The types of bacteria vary depending on the delivery method. Babies born vaginally had low C. difficule, an infection that can cause diarrhoea and intestinal problems in babies born via c-section. While those born vaginally had higher Bifidobacterium. Bifidobacterium is essential for proper gut function. Newborns who had skin to skin contact with their mother, immediately after birth, had higher levels of good bacteria compared with those that were separated at birth.

Birth can be unpredictable and c-sections can’t always be avoided. Many babies are born via c-section. To the c-section Mum’s, there are lots of other ways that can help your babies gut microbiome if you they were born via c-section.

antibiotic pills

  1. Antibiotic Use

Mothers who receive antibiotics during labour are also more likely to have changes in their and their babies gut microbiome. Antibiotics kill harmful microbes that cause infection, but they also wipe out the good bacteria. To read more about gut health in children and the best probiotics for kids.

woman breastfeeding newborn

  1. Feeding Method

What a baby drinks in the first few months or years, affects their gut microbiome. Breast milk is a very specialised food for babies and their gut bacteria. It includes protein, fat, carbohydrate and immunoglobulins. Mother’s milk is also easier to digest and gentle on the intestinal tract of the baby.  Breast fed babies have higher proportions of specific healthy bacteria.

Breast milk contains antibodies that can fight infection and give babies a head start in preventing and fighting infections. Formula fed babies, are more likely to have higher levels of pathogenic — or disease causing — bacteria. Formula also changes the pH level of the Gut, which can lead to an overgrowth of these pathogens.

There are lots of reasons why breastfeeding doesn’t always work out. To the Mums who are formula feeding your babies, there are lots of other ways that you can help your babies gut health so please don’t be overly concerned and chat to your integrative practitioner, nutritionist or naturopath if you have any worries to be addressed.

baby eating food

  1. Diet

Diet is the most relevant factor to influence the gut microbiome. Generally, its advised to wait for over 6 months before starting an infant on solids. Before that their guts aren’t matured enough to digest foods.

With infants it is important to:

– Encourage Dietary fiber (fruits, vegetables and other plants)

– Eat a varied the diet. Diversity of foods creates a diverse range of good bacteria. Healthy gut comes from a diverse range of gut bacteria.

A typical western diet does not include a varied range of gut flora, often because it is laden with processed and sugary foods.

When comparing children from Africa to children who eat a typical western diet, there is a marked difference in their gut flora. Those in Africa who were typically breast fed up to the age of 2 and then ate a plant based diet had a more diverse healthy gut flora compared to the children who ate a typical western diet.

Diet plays a huge role in gut microbiome and ensuring a wide range of wholefoods that support gut health is key.


How to boost the gut bacteria of a Baby:

Probiotics from Supplements:

Most probiotics for under 3 year olds are in powdered form and can be taken in the following ways:

  • Mixed with a small amount of breast milk and put on the nipple before breastfeeding.
  • Mixed with a small amount of breast milk and placed inside of the babies mouth. (ensure it’s a wet consistency not powdered form)
  • Added to formula feeds
  • Once the baby is eating solids, add to yoghurts.

It is best to work with a practitioner on a specific plan for you and your child’s needs, if you need more support.

Probiotics from food:

Fermented foods include live bacteria. Once a baby has begun eating solids foods, slowly add fermented foods. Good examples are live yoghurt, coconut kefir, fermented sweet potatoes and sauerkraut. In western cultures, the sour flavour is quite foreign. Fermented foods are a wonderful way to introduce sour flavours. Many children consume highly processed foods that are overwhelmingly sweet and salty. Sugar preference may also be linked to the type of bacteria in the gut. Giving fermented foods to children from an early age can actually lessen their desire to over consume sweet foods.

The key is to start slow. Dipping a spoon or finger in the juice of sauerkraut or other fermented vegetable and letting the baby taste it, slowly introduces the sour flavour into their diet. Include more fermented foods into their diet as they become accustomed to the sour taste.

If you’d like to learn some simple fermenting recipes for families, pop you name down here to be the first to know when the Fermenting for Families program kicks off!


Prebiotics promote the growth of our friendly bacteria by acting as their food source. Food sources include onions, garlic, under-ripe bananas, oats, artichokes, asparagus, leeks, psyllium, whole grain wheat, whole grain corn, and chicory.

Once a baby reaches the appropriate milestones for eating and solids are being introduced, prebiotics can be included.  Start slow and include small amounts of Oats, bananas, small pieces of whole wheat toast and soft-cooked asparagus.

By age 3, a child’s gut microbiota resembles that of the adult. These first 3 years are a super important time to establish a healthy diverse gut microbiome. Being aware of the 5 key areas above and implementing ways to boost your babies gut bacteria, can help build a strong foundation for their gut health.

Want some recipes to get started on? Download our Collaboration of recipes from the Gut Healing Community.


About Meagan

Meagan is the owner and founder of The Gut Healing Community. She loves nothing more than finding ways to support other families and give them the information she wishes she had, right from the start of her families’ healing journey. Meagan helps amazing Mum’s switch to eating a diet rich in wholefoods and reduce toxins in their lives to improve their gut health.



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