The following blog is written by nutrition work experience student Kyra, studying BSc Nutrition at the University of Hertfordshire. Click here to learn more about Clasado Biosciences and the team behind prebiotic supplement Bimuno.

Childhood is an extremely important period for all aspects of physiological development. This includes the maturation of the gut microbiome, the community of microbes that inhabit the gut. The first two years post-birth is when we see major changes to the gut microbiome and these changes can affect both the current and future health of the child1. The gut microbiome is a complex eco-system made up of trillions of bacteria and other micro-organisms that co-exist in the gut, but particularly in a small section of the large intestine known as the cecum1. The composition of bacteria in the gut microbiome tends to settle around the age of three. However, many factors can disrupt this which can cause unwanted side effects such as poor immunity and allergies. As the child grows, the microbiome shapes the development of the immune system by teaching it which pathogens to attack and which cells to leave alone2. The importance of this interaction is highlighted by the fact that 70-80% of the body’s immune cells are found in and around the gut2. The gut microbiome also plays a vital role in controlling digestion by breaking down nutrients into forms that can be more easily absorbed by the body3.

Intestinal bacterial colonisation begins when the foetus is in early development and the infant gut microbiome is properly established after birth4. A major factor contributing to the variation in the infant microbiome is the mode of delivery at birth. Birth by Cesarean section (C-section) tends to result in an infant microbiome more abundant in Staphylococcus, Corynebacteria, and Propionibacterium, with lower levels of Bifidobacteria and Bacteroides5. The gut microbiome of infants born surgically shows lower bacterial diversity. This is important, since in general, increased diversity of microbes in the gut is considered protective5. The presence of different types of bacteria occurs through vertical transfer as the infant passes through the birth canal. These differences in initial newborn communities may have health consequences since the genera Bifidobacterium and Lactobacillus are considered to be beneficial to the body, whereas some Staphylococcus spp. and Clostridium spp. have pathogenic potential6. Research has shown that the gut microbiome undergoes three distinct phases of progression. These are known as the Developmental phase, the Transitional phase and the Stable phase7.

Developmental phase (3-14 months)

The gut microbiome of a newborn is dominated by Enterobacteriaceae and Staphylococcus. The expansion of these bacteria leads to the gradual consumption of oxygen, which favours the growth of anaerobic bacteria such as Bifidobacterium and Clostridium4. The diversity of the gut microbiome remains narrow during early infancy and is predominantly Bifidobacterium (in the Actinobacteria phylum) and Lactobacillus until the introduction of solid foods8. The presence of this bacteria is linked to the consumption of Human Milk Oligosaccharides (HMO), as Bifidobacterium is responsible for the metabolism of oligosaccharides found in HMO; similar in structure to Galactooligosaccharides (GOS)8.

It has been estimated that 25-30% of the infant bacterial microbiome originates from milk (9), which indicates the specialisation of the infant gut microbiome to deal with a strictly milk based diet. If women are unable to breastfeed, it is recommended that the child is given formulas fortified with FOS and GOS to simulate HMO9. The next significant step-change in development is the introduction of solid foods at around 6 months. This stage sees a large shift in the gut microbiome composition, resulting in a higher bacterial load and diversity. After weaning, Bifidobacterium is outcompeted by adult-diet micro-organisms such as Bacteroides, Firmicutes, Clostridium and Prevotella8. These bacteria are better able to break down complex carbohydrates from solid foods, creating by-products such as short-chain fatty acids (SFCAs), a major source of energy for colon cells.

Transitional phase (15-30 months)

In the Transitional phase, the functional repertoire of an infant's gut microbiome will continue to change. The child’s diet of solid foods will promote the growth of bacteria that allow the utilisation of a larger variety of carbohydrates and other macronutrients in the diet. Bacteroides such as Prevotella will continue to develop as well as the species Proteobacteria4.  

Stable phase (>31 months)

Eventually, by around 3 years of age, the gut microbiome stabilises and the proportion of individual types of bacteria is similar to that observed in a typical adult gut microbiome8. It is commonly characterised by a higher bacterial diversity and predominance of Firmicutes species, such as Lactobacillus, Enterococcus and Clostridium8. The establishment of the gut microbiome will remain fairly stable throughout adult life in the absence of dysbiosis. Research has suggested that a disruption or dybiosis of the ‘normal’ gut microbiome can contribute to the onset of immune disorders in infants, such as allergies. Defined as an imbalance in the gut microbial community, dysbiosis could occur due to changes in the relative abundance of microbes8.

The effect of breastfeeding & weaning

The growth of the infant’s microbiome is heavily reliant on the consumption of breast milk as the oligosaccharides present promote the growth of Lactobacillus and Bifidobacterium10. Due to this, it is recommended that pregnant women breast feed their child for as long as possible, as low levels of Bifidobacterium are associated with atopic disease and a weakened immune system11. The diets of children being weaned may also have a significant influence on gut microbial diversity, as research has shown that high carbohydrate diets lead to an increase in Prevotella. Conversely, high fat and high protein diets promote the development of the Bacteroidetes phylum12.

Much like the adult population, fibre should be a key aspect of the infant’s diet as it is beneficial for the composition of the gut microbiome. A balanced diet during infancy is essential for the development of a healthy gut as lower bacterial diversity is associated with negative health outcomes. It is recommended that solid food is introduced for babies at around 6 months of age. This diet should include a wide range of minimally-processed foods such as vegetables, wholegrains, fruits and pulses such as beans and lentils. These are all rich in vitamins and good sources of non-digestible fibre that aids in a healthy digestive system and feeds the healthy bacteria in the gut microbiome13. In most cases, symptoms of food sensitisation appear when solid foods are introduced during the weaning process. Microbial colonisation of the gut microbiome has been shown to be important in the development of Th1 and regulatory T cells, which are necessary to maintain immunologic balance and promote tolerance to foods14.

The gut microbiome of children with food allergies tends to be less diverse and associated with delayed colonisation of Bacteroidetes, Bifidobacterium and Lactobacillus15. Bifidobacterium has been reported to directly correlate with the amount of IgA secreted and to have anti-inflammatory effects. Therefore, lower levels of bifidobacteria are associated with a weakened immune system16. In children, estimates of food allergy range from 1% to 8%, with the highest prevalence in the first year of life4. They commonly present during infancy with the intake of milk, eggs, peanuts and wheat. However, emerging evidence has shown that early introduction of allergenic foods, specifically peanuts, can be protective against the development of food allergy.

In conclusion

The infant gut microbiome is gradually established during the first 3 years of life and breast feeding is considered the optimal feeding mode for infants in order to establish a healthy gut microbiome. How an infant’s gut microbiome is nourished and supported has a clear long term influence on physical health and wellbeing. However, the development of the gut microbiome is not fixed. The development varies by individual and multiple factors can affect the presence of certain gut microbes such as birth mode, complementary feeding, medication use and food allergies. Following this, a balanced diet including sufficient intake of fibre during the weaning period is important for diversity, immune function and development in childhood.

  1. The Human Microbiome and Child Growth – First 1000 Days and Beyond, Robertson et al, Trends in Microbiology, 2018,
  2. The role of the gut microbiota in immune homeostasis and autoimmunity, Wu et al, Gut Microbes, 2012,
  3. Gut microbiota functions: metabolism of nutrients and other food components, Rowland et al, European Journal of Nutrition, 2017,
  4. Development of the gut microbiota in infancy and its impact on health in later life, Tanaka et al, Allergology International, 2017,  
  5. The infant microbiome: Implications for Infant Health and Neurocognitive Development, Yang et al, Nursing Research, 2016,
  6. What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet and Diseases, Rinninella et al, Microorganisms, 2019,
  7. Temporal development of the gut microbiome in early childhood from the TEDDY study, Stewart et al, Nature, 2018,
  8. The Gut Microbiota in the First Decade of Life, Derrien et al, Trends in Microbiology, 2019,
  9. The Human Microbiome and Child Growth – First 1000 Days and Beyond, Robertson et al, Trends in Microbiology, 2018,
  10. Dysbiosis, Hedayat et al, 2020, The Theory of Endobiogeny,
  11. Shaping the Gut Microbiota by Breastfeeding: The Gateway to Allergy Prevention? Van den Elsen et al, Frontiers in Pediatrics, 2019,
  12. Gut Microbiome and the Development of Food Allergy and Allergic Disease, Prince et al, Pediatric Clinics of North America, 2015,
  13. Gut Microbiota diversity according to dietary habits and geographical provenance, Senghor et al, Human Microbiome Journal, 2018,
  14. Foundations in Human Nutrition, Mann & Truswell,  
  15. Gut Microbiome and the Development of Food Allergy and Allergic Disease, Prince et al, Pediatric Clinics of North America, 2015,
  16. Microbial and Nutritional Programming - The Importance of the Microbiome and Early Exposure to Potential Food Allergens in the Development of Allergies, Cukrowska, Nutrients, 2018,

Our latest blog posts

For Healthcare Professionals

View all

More for Healthcare Professionals

Our Products


This section is an information and educational resource for healthcare professionals. It is not intended for consumers. If you wish to purchase Bimuno please click here