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Linking the microbiome and colic

When supporting colic in babies, it is important to address the microbiome. This not only affects colic and wind in their present health but also helps to support their overall future health. In this post I will touch upon some of the key topics relating to the microbiome that are connected to the development of colic but this is by no means a full list and there are other causative factors relating to nutrition to look into. If you are a parent reading this then please don’t worry about antibiotic exposure, them being born c-section and/or if you are aware that you may have digestive issues that could play a role. Colic has no known single solution for all babies and the causes are multi-factorial. It is important to be aware of the potential triggers so that we can take a holistic approach to addressing the problem. If you would like support to help address colic in your baby then please contact me for more details. Although seemingly a digestive problem- improving symptoms of colic is not just about supporting digestion in the baby but it is an easy place to start and by doing so it will also help to create a stronger foundation for the baby to grow upon.


Antibiotics are known to upset adult digestion and it is not different for babies. Antibiotics alter a baby’s microbiome and babies with colic have an altered microbiome so it can worsen an existing imbalance if not the main cause. The mother’s microbiome also needs to be considered. A study in 2020 concluded that it came as quite a shock that even just one day of antibiotics was associated with profound changes In the microbiota of breast milk. Antibiotics pass to the baby via the bloodstream during pregnancy , at birth and via breast milk. Vaginally delivered babies from mothers that had antibiotics gained 25% of their bacteria from their mother whereas babies from mothers that had not had antibiotics gained 72%! Don’t get me wrong-antibiotics are lifesavers. I can’t stress that enough despite their negative impact on the microbiome. The take-away from this is that by understanding the gut microbiome of the mother taking into consideration antibiotic exposure along with the antibiotic exposure of the baby, this can help when supporting colic.


C-section is probably the most well-known factor for having an effect on babies as they don’t pick up the bacteria from the mothers’ birth canal. C-section has much research demonstrating it increases the chance of colic and other allergy type health conditions like food allergy, eczema and asthma. However, I would question a lot of this research in terms of the lack of consideration regarding possible inclusion of antibiotics as a major contributing factor to the results post surgery. The first flora is acquired from contamination or inoculation from the environment the baby is born into. Via a vaginal birth the baby is exposed to the vaginal, skin and rectal microbiota of the mother whereas via c-section the baby is exposed to the skin and hospital environmental biota. Babies born via vaginal birth for that reason are found to be much more dominant in supportive lactobacilli.

A mother’s gut bacteria-

The actual bacteria in a mother’s gut is the bacteria that transfers into her breast milk and then into her baby’s gut. Looking after the mother’s digestion is therefore vital so she can pass bacteria to her newborn. Also, the mother’s breast milk provides food for a baby’s gut bacteria to thrive in the form of Human Milk Oligosaccharides. This recent study supports us helping mothers to eat well as the foods she eats during lactation can shape the functional abilities of milk bacteria via the profile of these human milk oligosaccharides. There are also correlations between the fecal bacteria quality of the mum and the fecal bacteria quality of the baby. Recent research has shown that a baby DOES have bacteria in their gut before delivery. This is great news because it means that by supporting the gut health of the mother whilst pregnant through diet and appropriate supplements, we can support the child’s gut health whichever way they are born and it will help with ongoing nourishment if breastfed.

Whatever the situation, the last thing I want my supermums to feel is guilt or shame. We all do the best we can as mums and no matter what the situation, there is always so much we can do with Nutritional Therapy to help support their current and future health.

I am a registered Naturopathic Nutritional Therapist and specialist in Clinical Paediatric Nutrition. If you are interested in starting Nutritional Therapy for yourself, your family or your child then please contact me for more information/FREE discovery call or you can check out my services on my website.

1. Asbury, MR et al. 2020. Mothers of preterm infants have individualized breast milk microbiota that changes temporally based on maternal characteristics. Cell Host & Microbe, 28 (5), pp.669-682.

2. Weizhong, L et al. 2020. Vertical transmission of gut microbiome and antimicrobial resistance genes in infants exposed to antibiotics at birth. The Journal of Infectious Diseases, XX.

3. Parnanen, K et al. 2018. Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. Nat Commun, 24(9).

4. Stinson, LF et al. 2019. The not-so-sterile womb: evidence that the human fetus Is exposed to bacteria prior to birth. Front Microbiol.

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