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How To Set Up Good Gut Health In Your Baby for Life

By now you probably know or have at least heard about the importance of your microbiome for overall health. If not, it’s time to start paying attention. 

Your microbiome is the mini-ecosystem of microorganisms that make up ~90% of the human body. Our whole bodies are covered in microorganisms, but the majority of them reside in the large intestine in our gut. Gut microbes are key to many aspects of our health including immune, metabolic and neurobehavioral traits. For us to be as healthy as possible, we need our microbiome to be as diverse and balanced. You can’t have one without the other. 

Therefore when it comes to setting up our child's health, making sure we do as much as possible to support the establishment of their microbiome is one of the best starts to your child’s future health. The research over the past decades has found that the gut microbiome can shape their metabolic, neurologic and immune health as well as their risk for chronic diseases later life. 

Here are my recommendations for what you can do in pregnancy and beyond to support the establishment of a diverse and healthy microbiome in your child.

Make sure you investigate and resolve any gut issues you may have before falling pregnant. Suspect you have parasites, allergies or intolerances? Work with someone who can help you identify any underlying dysfunction that may be preventing your gut from functioning optimally. We know that both the mother and fathers microbiome influences a child’s microbiome, so you want to make sure your gut is as healthy as possible before to trying to fall pregnant. Starting by eating a diet rich in a variety of plant foods is a good start.

Choose a vaginal delivery if possible. Sometime easier said that done! While in an ideal world I think most ladies would opt for a vaginal delivery. The vagina is abundant with good bacteria which can set up you baby for life. C-section born babies will be exposed to the skin microbiome of the hospital staff or people that deliver them. There is a practice know as “seeding” that can help to expose your baby to some to the healthy vaginal microbiome. It is done simply by inserting a sterile gauze into the vaginal for around 1 hour to absorb all the healthy vaginal bacteria (predominately lactobacillus species). The gauze is the use to wipe all of the newborn baby, or “seeding” it. Seeding should be undertaken with the guidance of an experienced midwife, double or doctor. You just want to make sure you are group B streptococcus negative before undertaking seeding. Preparation and planning are key, so perhaps putting this in your birth plan in case things don't go as originally planned.

Supplement with a probiotic during pregnancy and whilst breastfeeding. Based on the latest research, I recommend that mothers take a pregnancy-specific probiotic throughout the second and third trimester, as well as while they are breastfeeding. For mothers that aren’t breastfeeding, probiotics should be given directly to the baby for the first year of life. There are many pregnancy probiotic supplements out there so it is important to make sure you are looking for a good one. Ideally, you need to be taking one that contains the strains Bifidobacterium and Lactobacillus GG with upwards of 10 billion CFU’s (“Colony Forming Units”-the measurement amount of a bacteria). Probiotics given to infants should be infant specific with the same species as mentioned above for mothers.

If you can, breastfeed. Breast milk contains proteins, fats, carbohydrates, vitamins and minerals plus non-nutritional components including antimicrobial factors, digestive enzymes, hormones, immune-related compounds and growth factors. The main carbohydrate in breast milk is lactose. Lactose not only acts as a source of energy for baby but also as fuel for bacteria in helping to establish a healthy gut flora. The fats found in breast milk are predominately essential fatty acids (EPA & DHA) and long chain polyunsaturated fatty acids. These fats are essential for the development and health of the brain as well as structure and function of cell membranes in every part of the body.

While the macro-nutrient profile of infant formula is similar to breast milk, it lacks all the digestive enzymes, immune and growth factors that breast milk contains. Formula fed babies in general suffer more upper respiratory infections, diarrhoea and, later in life, higher rates of allergies and asthma than breastfed babies. As infant formula lacks probiotic bacteria, I always ensure that fermented foods rich in probiotic bacteria are included as first food such as yogurts. A lack of good bacteria can leave baby open to infections, a compromised immune system, potential allergies and constipation or diarrhoea.

Offer a diversity of different plant-based foods. As soon as it is time to start introducing solid foods you want to be thinking about offering a diversity of different vegetables and fruits. The more variety, the better the diversity of bacteria in the gut in with fuel. When age-appropriate, focus on including vegetables that are high in prebiotics such as leeks, artichoke, chickpeas and lentils as they will help to ‘feed’ the good bacteria in their gut. 

Introduce them to food sources of probiotics. Fermented foods are rich in probiotics, which feed the beneficial bacteria in your gut and help to improve the overall health of the microbiome. The best way to include these is to start by adding small amounts into purees. Try mixing in a little dash of natural whole milk yoghurt, kefir or 1 tablespoon of sauerkraut juice.

Go organic, where possible. Our microbes and their genes are very sensitive to chemicals, so consuming foods that are made with chemicals and heavily sprayed with pesticides can lead to disruption in their metabolism and the important chemicals they produce, which affects the health of our microbiome and in turn, us. Check out the Environmental Working Groups ‘Dirty Dozen’ Guide to help you prioritise what to buy organic and what products are safe to buy conventional. 

Avoid over sanitising. While being clean is fine, overly sterile environments don’t promote the biodiversity of your gut bacteria. Don’t be afraid of getting dirty and skip the hand sanitiser. Washing your hands well with warm soapy water for 30 seconds has been shown to inactivate the influenza A virus quicker than disinfectants. 

Take them out in nature. Many new mothers are understandably very projective of their babies and want to shelter them away at home from any potential germs or danger. However, exposing your child to the outdoors and to friends and family members will help them to build a stronger microbiome. Obviously, we don’t want to be passing bub to anyone that is contagious, but we do want to be making sure children are given the opportunity to pick up lots of ‘good’ bacteria from lots of different places and people. 

Don’t have enough stress already with a newborn? Why not get a pet! Studies have shown that babies who grow up in houses with animals (particularly dogs and cats) have a more diverse microbiome and a reduced risk of allergies, eczema, diabetes and needed fewer courses of antibiotics in the first year of life. If a pet isn’t an option for you, don’t be afraid to take your child to places where there are trusted pets, such as a family or friends house, or a local park. 

Avoid unnecessary antibiotics. Just to be 100% clear, antibiotics are amazing. They are lifesaving and we are so lucky to have them. However, the problem we have is that they are often overprescribed, especially in children. In instances of viral illnesses antibiotics are completely ineffective and therefore usually end up doing more damage than good. We now know that the occasional round of antibiotics is tolerated by a healthy microbiome, but the recurrent rounds that can disrupt our microbial diversity and balance, as well as increasing our risk of other infections. 


Baldassarre, M. E., Palladino, V., Amoruso, A., Pindinelli, S., Mastromarino, P., Fanelli, M., … Laforgia, N. (2018). Rationale of Probiotic Supplementation during Pregnancy and Neonatal Period. Nutrients, 10(11), 1693. doi:10.3390/nu10111693

Binns, C., Lee, M., & Low, W. Y. (2016). The Long-Term Public Health Benefits of Breastfeeding. Asia Pacific Journal of Public Health, 28(1), 7-14. doi:10.1177/1010539515624964

Hesselmar, B., Hicke-Roberts, A., Lundell, A., Adlerberth, I., Rudin, A., Saalman, R., … Wold, A. E. (2018). Pet-keeping in early life reduces the risk of allergy in a dose-dependent fashion. PLOS ONE, 13(12), e0208472. doi:10.1371/journal.pone.0208472

Hirose, R., Nakaya, T., Naito, Y., Daidoji, T., Bandou, R., Inoue, K., … Itoh, Y. (2019). Situations Leading to Reduced Effectiveness of Current Hand Hygiene against Infectious Mucus from Influenza Virus-Infected Patients. mSphere, 4(5). doi:10.1128/msphere.00474-19

Schulfer, A., & Blaser, M. J. (2015). Risks of Antibiotic Exposures Early in Life on the Developing Microbiome. PLoS pathogens, 11(7), e1004903. doi:10.1371/journal.ppat.1004903

Valdes, A. M., Walter, J., Segal, E., & Spector, T. D. (2018). Role of the gut microbiota in nutrition and health. BMJ (Clinical research ed.), 361, k2179. doi:10.1136/bmj.k2179

Wang, H. T., Anvari, S., & Anagnostou, K. (2019). The Role of Probiotics in Preventing Allergic Disease. Children (Basel, Switzerland), 6(2), 24. doi:10.3390/children6020024

The information contained in this article is for informational and educational purposes only.

We cannot guarantee that any information found in this article, will work as advertised, nor that they will give you the desired results. Individual results may vary.

None of the information contained in this article is intended to diagnose, treat, alleviate or relieve any medical or health conditions nor serve as a substitute for the advice provided by your physician or other healthcare professional.

You should always speak with your physician or other healthcare professional before adopting any treatment for a health problem or undertaking any new dietary regime. If you have or suspect that you have a medical problem, or you should contact your health care provider.

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