How your microbiome is formed

Author: Dr Gregory Crocetti

14 November 2018 Education
Women with infant child under 3 years of age, when the microbiome is formed.

In recent years, scientists have discovered that the microbes in the human gut contribute a range of vital functions associated with good health, including producing many of our vitamins, educating our immune system and more. But how do they get in there…and where do they come from?

The development of our microbiome is a dynamic process

As an infant, we inherit our first microbes from our mother. For many people, they are seeded with bacteria from their mother’s vagina and faeces as they enter the world through the birth canal1, although mounting evidence suggests that our first contact with microbes may occur in the womb. Immediately afterwards, we encounter beneficial microbes on our mother’s skin and in her breast milk2. These early microbes trigger special cells in our gut to release mucus3 – providing the perfect habitat for bacteria and other microbes to anchor themselves and start interacting with our gut.

As toddlers, we rely on a rich diversity of gut bacteria to help us consume an increasingly complex diet of solid foods. On its own, the human gut does not have the ability to break the chemical bonds in fibre-containing foods. Instead, we rely on our resident gut microbes to break down fibre, providing us with valuable nutrients, vitamins and energy – essentially the building blocks for a growing body.

Microbiome development in the early years of life

The first thousand days3 of our lives is now considered the critical window of development for our gastrointestinal, immune and nervous systems – and our gut microbiome plays a key role in this process. Emerging research shows that disturbances to the gut microbiome during this early period (particularly through the use of antibiotics) are associated with poor health outcomes later in life, such as eczema, asthma, inflammatory bowel diseases and more4.

By around three years of age, it is thought the community of microbes in our gut reaches maturity. From this point, it can be difficult to disrupt the overall makeup of our ‘adult’ microbiota, although a course of antibiotics can have a significant impact5 – and it can take several months6 for our gut microbiota to begin to recover from the disturbance.

Where else do our microbes come from?

It is thought our microbes come to us from a wide range of sources, such as other people, animals, soil, plants, furniture, clothing, buildings…even the air we breathe. Recent studies have linked lower levels of childhood allergies with the presence of siblings, pets or growing up on a farm7 – suggesting that these might be important sources of microbial diversity in our early lives. But the single largest source of microbes entering our body is through the food we eat – with the average human swallowing around a million microbes in every gram of food.

You are what you eat

Diet is increasingly understood as one of the most important factors in shaping the composition and function of our gut microbiota throughout our lives –with both short and long-term nutritional studies8 suggesting great potential for preventing and treating a range of chronic and gut-related diseases. Eating a diverse diet with sufficient amounts of fibre – including fruits, vegetables and whole grains – is a great way to promote a healthy gut microbiome and improve overall gut health.


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Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.
Proceedings of the National Academy of Sciences, 107(26), 11971-11975 (2010). Doi: 10.1073/pnas.1002601107

2). Le Doare, K., Holder, B., Bassett, A., & Pannaraj, P. S.
Mother’s milk: A purposeful contribution to the development of the infant microbiota and immunity.
Frontiers in immunology, 9, 361 (2018). Doi: 10.3389/fimmu.2018.00361

3). Wopereis, H., Oozeer, R., Knipping, K., Belzer, C., & Knol, J.
The first thousand days – intestinal microbiology of early life: establishing a symbiosis.
Pediatric Allergy and Immunology, 25(5), 428-438 (2014). Doi: 10.1111/pai.12232

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The role of early life nutrition in the establishment of gastrointestinal microbial composition and function.
Gut Microbes, 8(2), 143-171 (2017). Doi: 10.1080/19490976.2016.1278104

5). Ferrer, M., Martins dos Santos, V.A.P., Ott, S.J., Moya, A.
Gut microbiota disturbance during antibiotic therapy.
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6). Raymond, F., Deraspe, M., Boissinot, M., Bergeron, M.G. & Corbeil, J.
Partial recovery of microbiomes after antibiotic treatment.
Gut Microbes, 7(5), 428-434 (2016). Doi: 10.1080/19490976.2016.1216747

7). von Mutius, E.
The microbial environment and its influence on asthma prevention in early life.
The Journal of Allergy and Clinical Immunology, 137(3), 680-689 (2016). Doi: 10.1016/j.jaci.2015.12.1301

8). Sheflin, A.M, Melby, C.L, Carbonero, F. & Weir, T.L.
Linking dietary patterns with gut microbial composition and function.
Gut Microbes, 8(2), 113-129 (2017). Doi: 10.1080/19490976.2016.1270809