You’d have to have been living under a rock for the last few years to not have heard about the wonders of “the microbiome”. It’s a fascinating area of scientific research, one I am active in as a researcher so I completely understand the charm! In the world of parenting ‘microbiome’ has become a bit of a buzzword; some healthcare professionals are now considering the impact of different interventions on the infant gut microbiome and – rightly or wrongly – are making recommendations accordingly.  If you’re wondering what the microbiome actually is, and questioning how it might affect your baby’s health, you’re not alone. Here, I’ve compiled answers to some of the most common questions parents ask us about the microbiome.

What actually is the microbiome?

We are not alone. Every single one of us carries billions of bacteria, fungi, viruses and other microscopic organisms on and in our bodies. Whilst that sounds a bit yuck, it’s all perfectly natural and it’s something that both we and the micro-organisms have evolved to live with. In layman’s terms we use the word ‘microbiome’ to refer to all those micro-organisms. Some people like to point out that ‘microbiota’ is a more technically correct term, with ‘microbiome’ referring to the microbes and their genes. However, these terms are often used interchangeably1 and microbiome is commonly understood to apply to both situations.

Because each of us have a different collection of bugs on and in us, each of us has our own, unique microbiome. Our microbiome also changes with time and in response to different things.

What kind of things influence your microbiome?

So far, scientists have identified a number of factors that can influence a person’s microbiome. They include; genetics, sex, age, health conditions, stress, what medicines you take, how you were born, where you live, what you eat and drink, your exercise regime, whether or not you have pets and even having sex! In an effort to determine what a ‘normal’ adult gut microbiome was, the scientists involved in The Belgian Flemish Gut Flora Project have identified 69 factors that influence it, the largest of which was the shape and consistency of the stool sample provided!2

Is my baby doomed if I had a C-section or formula fed?

The short answer is no. Studies have shown differences in the gut microbiome between babies born by C-section compared to vaginally born babies but a recent review concluded that it’s likely to be the underlying factors associated with the need for a C-section and not the lack of exposure to vaginal microbiota that results in a difference in infant gut microbiota3.

Similarly, when babies who are formula fed are compared with breastfed babies, some studies find the composition of the microbiota differs. When you consider that what you eat and drink can impact gut microbiota, this isn’t surprising. What’s not clear is whether small amounts of formula supplementation have any impact on gut microbiota; claims that just one bottle will cause “irrevocable damage to your baby’s immature digestive system” are thus far unsubstantiated.

We don’t really know if differences in gut microbiota associated with mode of birth or feeding persist into toddlerhood and beyond, or if they lead to increased risk of health issues in later life.  In the Belgian-Flemish study mentioned above the scientists concluded that

“early-life events that are generally thought to affect adult microbiota composition were not associated with microbiota composition variation in our study, including mode of birth, place of birth, and infant nutrition (breastfed or not breastfed)”2.

What can I do to ensure my baby has a healthy microbiome?

Well, first up, talk to your Doctor if you have any concerns about your baby’s health or wellbeing. Based on current evidence, my opinion as a scientist is that if your baby was delivered by C-section and/or you fed them formula, there’s no need to worry. Yes, the microbial composition of their gut may be different to their vaginally born or breastfed peers, at least for the first few months of life, but there’s no guarantee that this will have any negative impact on their future health or wellbeing. Just to be sure, you could always get a dog!



    Ursell LK, Metcalf JL, Wegener Parfrey LW, Knight R. (2012). Defining the human microbiome. Nutrition Reviews, 70 (Suppl 1): S38-S44.
  • Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust 2, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D’hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J. (2016) Population-level analysis of gut microbiome variation. Science, 352(6285):560-564.
  • Stinson LF, Payne MS, Keelan JA. (2018) A Critical Review of the Bacterial Baptism Hypothesis and the Impact of Cesarean Delivery on the Infant Microbiome. Frontiers in Medicine, 04 May 2018;


Thank you to Dr Jolinda Pollock, Prof Mick Watson, Dr Samantha Lycett and Dr Andy Law for helping me translate the complexities of microbiome.

Header image ‘E.-coli Bacteria’ by NIAID CC-BY-2.0