Healthcare Professionals

The Gut Microbiome and Weaning – The Early Years

Nutrition is vital for growth and development during the first 1000 days of life and can influence health throughout the normal human lifespan. Milk and gradual introduction of solid food (weaning), provide the only sources of nutrition during this time. Nutrients provided to an infant not only provide essential macronutrients but also shape and form the collection of bacteria and other microbes in the gut – known as the gut microbiome – and in turn, future health outcomes.

The gut microbiome is involved in many physiological processes in the human life cycle and is associated with development and immunity for numerous reasons. Due to the importance of the gut microbiome to the body, it is crucial to cultivate a deeper understanding of how it develops during infancy and in childhood(1).

Development of the gut microbiome

The bacterial colonisation of an infant’s gut microbiome has nutritional, physical and medical influences. The mode of delivery during birth is shown to affect which microbes are in abundance in the gut microbiome of new-borns. For example, new-borns delivered vaginally have microbes from the genera Bacteroides, Bifidobacterium, Parabacteroides and Escherichia/Shigella.

At 4-12 months of age, the difference between gut microbiome composition dependent on delivery mode gradually decreases, but those born via caesarean-section (c-section) are shown to have a less optimal gut microbiome composition, due to the types of bacteria introduced at birth. Additionally, infants that are exclusively breastfed also tend to have a higher prevalence of probiotics, types bacteria that are recognised to benefit the gut (2).

Cessation of breastfeeding seems to begin a shift in the gut microbiome of 12-month-old infants towards a more adult-like composition. Over time, there appears to be a more complex development of the gut microbiome of infants and their compositions become more alike. By the age of 3, we begin to see this more mature microbiome composition. It is the end of breastfeeding, rather than the introduction of solid foods, that seems to begin the maturation of the gut microbiome of infants (2).

While it was always thought that babies were born without a microbiome, research suggests that microbes are present in the placenta, however the influence of microbes in prenatal life is not yet clear (3). There is evidence that the foetus inherits the mother’s microbes even before birth. This research has been conducted using molecular methods and therefore cannot yet be confirmed to happen in humans.

For this reason, the development of the gut microbiome, from types of birth, feeding modes and geographical location are more commonly used as an explanation for the diversity in gut microbiome development in infants (1). During toddler years, the type of full adult diet that the child is introduced to – for cultural, geographical or religious reasons – will shape the gut microbiome of the child, along with their exposure to antibiotics and other medications (4).

Implications of nutrition

The development of the gut microbiome may have an impact on both infant health and health outcomes later in life. A reduced diversity in the intestinal microbiome has been shown in infants with eczema, and allergic asthma is suggested to have an association with children’s gastrointestinal (GI) microbe community in early life.

Early life is a critical stage for immunological and microbiological development. For example, the c-section delivery mode appears to lead to a less favourable gut microbiome composition with reduced diversity, as well as an association with these children developing eczema or asthma (1).

The type of feeding that infants are exposed to has an impact on the gut microbiome. Breastfeeding is associated with a lower risk for obesity in later life, increased resistance to infection and decreased risk of allergies.

A natural prebiotic in breastmilk is Human milk oligosaccharides (HMO), which are types of nutrients that are not directly digested by the body, but feed microbes within the GI tract. This leads to the proliferation of bifidobacteria and lactobacillus, which in turn results in the production of short-chain fatty acids (SCFAs).

SCFAs maintain homeostasis within the gut microbiome. The gut microbiome is thought to help modulate the immune response and therefore could shape future response to disease (4). To replicate this effect, synthetic HMOs are often added to formula.

The change from breastfeeding to solid foods also has an influence on the kinds of bacteria that are found in the gut microbiome, as the gut adapts to the new nutrients available. Different nutrients feed different types of bacteria; the more beneficial kinds tend to prefer a variety of carbohydrate sources.

Implications of environment

The rise in autoimmune and atopic diseases in industrialised society has increased in recent decades. Epidemiological data suggests that environmental changes to the way we live has reduced our exposure to microbes during infancy.

Those who are exposed to pets or siblings, attend group care at an earlier age, or are raised on farms, have a lower incidence of atopic diseases (5). Dysbiosis of the gut microbiome, where there is an imbalance in the composition of the gut bacteria, is associated with inflammatory and non-communicable diseases across the life span (6).

Additionally, the early use of antibiotics can alter the balance of the gut microbes. There is an association between early use of antibiotics and possible long-term health implications. The association has a dose-response. Because of this, supplementation of prebiotics and probiotics in the diet of formula fed infants and young children is recommended for the maintenance of the gut microbiome (5).  Most commercially available brands include these ingredients in their products.

A negative alteration of the early gut microbiome shows an association with immune pathologies ranging from eczema, asthma and type 1 diabetes, to Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease (IBD) and even metabolic disorders such as obesity and type 2 diabetes (7).

Weaning and the gut microbiome

Health benefits can be gained from early life intervention in the development of the gut microbiome in infants. Focusing on the establishment of the infant gut microbiome and its development into a mature gut microbiome is important, particularly where this is prevented or challenged due to environmental or medical reasons (7).

The dietary intake of infants and young children is vital to the maintenance of the gut microbiome for two reasons. It is the cessation of breastfeeding that appears to be an important consideration in the change of the infant’s gut microbiome to a more adult like composition (2). We know that diet is a key modulatory factor in gut microbiome composition (6).

Exclusive breastfeeding or an appropriate formula feed is recommended for the first six months of life and both will provide the prebiotic carbohydrates (HMO, FOS and GOS, respectively) necessary to feed beneficial gut bacteria.

For healthy growth and development, introduction of solid food should begin from six months and this gradual transition can happen from six months to one year. The introduction of solid food is known as complementary feeding. Formula or breastmilk can be replaced with dairy at one year of age, alongside solid food (8). The World Health Organisation (WHO) recommends that breastfeeding can continue alongside solid food for children up to two years of age.

At first, the introduction of solid foods focuses on how theinfant learning how to eat, as well as increasing nutrient and energy intake (9). As time goes by, introducing a variety of foods from different food groups help the baby learn about different flavours and textures and the variety of foods will feed the gut microbiome. This mirrors how adults should aim for variety in their diet to feed the gut microbiome through different plant sources.


The first 1000 days are important in the development of a child’s gut microbiome and immunity. Alterations in the gut microbiome during this time are associated with inflammatory and autoimmune conditions later in childhood. Environmental and medical factors, including diet, can demonstrate the development of a rich and diverse gut microbiome, supporting the need for adequate nutrition from the beginning of a child’s life and beyond.

Future interventions using supplementary prebiotics and probiotics require more contextual research in early life and gut microbiome development, particularly when medical and environmental challenges are faced, such as repeated prescription of antibiotics in the first five years of life.


  1. Intestinal microbiota and its influence on childhood health
  2. Dynamics and stabilization of the human gut microbiome during the first year of life
  3. The composition of the gut microbiota throughout life, with an emphasis on early life
  4. The microbiome in early life: implications for health outcomes
  5. Early development of the gut microbiota and immune health
  6. Impact of Gut Microbiota Composition on Onset and Progression of Chronic Non-Communicable Diseases
  7. Health benefits conferred by the human gut microbiota during infancy
  8. NHS start for life – weaning

9.What to feed your baby baby/around-6-months/#anchor-tabs

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