The Gut Microbiome: Effect on Immunity in Infants & Children

The human gut has many essential roles. The most commonly known function is to transport, digest and absorb nutrients from the foods we eat.

Today, emerging evidence suggests the gut may also have an equally important role in the development and function of our immune system via both intestinal immune cells and gut bacteria.

gut microbes


The gastrointestinal tract in early life


The lining of a newborn baby’s intestine (the gastrointestinal tract) is made up of a single layer of cells known as the intestinal epithelium. The intestinal epithelium not only provides a physical barrier against harmful microbes that enter the gut, but it is also known to host the body’s largest population of immune cells.[1]

To put the volume of immune cells in the gut into perspective, the large intestine, also commonly known as the colon, is now recognized as the largest immune organ in the human body. [2] The gastrointestinal tract is also home to over 100 trillion bacteria, collectively known as the gut microbiota.[3]

Previously, it was thought that an infant’s intestine was sterile until birth and that the development of the microbiota only occurred following delivery. Findings from recent papers, however, have challenged this concept and suggest that bacteria are actually present in utero and the development of an infant’s microbiota begins before birth.[4]

Research further suggests that the microbiota of infants differs greatly depending on factors including the gestational age at birth, how the baby was born (vaginal or caesarian section) and feeding method (breastfed or formula-fed). [5]

In a 2016 review on the infant’s microbiome, it was found that the most common bacteria of breastfed infants is Bifidobacterium, whereas exclusively formula-fed infants exhibit an entirely different profile of bacterium.[6]

Breastfeeding and vaginal delivery were also found to be associated with a lower incidence of immune-related disorders, highlighting the potential impact of a microbiota profile on disease prevention.

Furthermore, children with severe acute malnutrition (an extreme form of undernutrition and growth faltering) have been found to have significantly lower microbiota diversity when compared to healthy children, further highlighting the role that microbiota may play in maintaining health, growth and development in children specifically. [7]

gut microbiome in infants


The gut microbiome and health


From the evidence above, we can see that the important role of microbiota in promoting health and preventing the risk of disease from birth is becoming increasingly clear.

In a recent review focusing on the impact of the gut microbiome on infant health outcomes, the gut microbiota was found to maintain and support health in three primary ways: [8]

The first role of the gut microbiota in supporting health is to act as a direct barrier against the growth of pathogenic organisms. This is achieved by competing for attachment sites in the intestinal lining and competing for nutrient availability.

Put simply, the greater the diversity of our microbiome, the harder it becomes for harmful bacteria to flourish because there are fewer nutrients available for the foreign bacteria to survive off.

The second role is in the digestion and metabolism of foods we consume from birth through to adulthood.

Bacteria are essential for the breakdown of carbohydrates, into short-chain fatty acids, which acts as an essential source of energy in keeping our intestinal cells healthy.

Animal studies have begun to reveal the role that the bacteria in our gut play in regulating the turnover and growth of intestinal epithelial cells, specifically for immune cells.

Research has shown that animals bred in a germ- free environments have been found to have overall lower densities of immune cells in the gut[9] when compared to animals bred in environments in which they are naturally exposed to bacteria.

Lastly, microorganisms in the gut are needed for the absorption of calcium, magnesium, and iron,[10] three minerals that play an essential role in energy metabolism and immune function.

microbiome immunity infants


The role of probiotics in infants and children


Given the important role that our gut microbiome plays in regulating our immune system, the routine use of probiotics has become increasingly popular today – especially for conjunctive use with antibiotic treatments.

A big challenge, however, when looking at the role of probiotics – is defining a ‘normal’ microbiota profile. As mentioned earlier, our microbiomes are constantly changing based on our environment and have been found to vary greatly between gender, ages and geographical areas.

So, is the routine use of probiotics really necessary in children? And what role do probiotic supplements really play?

In a large 2017 review focusing on the use of probiotics in children, it was concluded that only certain probiotic strains (Lactobacillus rhamnosus GG and Saccharomyces boulardii) may be effective in reducing the incidence of infection in children [11].

These findings were further supported by a large meta-analysis whereby the use of probiotics was also found to reduce the risk of infection in children.

However, a big limitation of the meta‐analysis was that there was no strain‐specific use of probiotics. Therefore, no recommendation can be convincingly made on the specific type of probiotic to use on a routine basis.[12]




In summary, it is clear that the gut microbiota plays a key role in maintaining and supporting health, by providing a direct barrier to the growth of harmful bacteria, providing energy to maintain the health of our intestinal cells and enabling the absorption of nutrients that play an important role in the maintenance of our immune systems.

Lastly, there is currently not enough clinical evidence to support the routine use of probiotics in children. The current guidelines highlight that not all probiotic strains have the same efficacy and only specific probiotic strains with proven efficacy and safety should be recommended for selected clinical conditions under medical supervision.

probiotic use for infants and children




[1] Lazar, V., Ditu, L.-M., Pircalabioru, G. G., Gheorghe, I., Curutiu, C., Holban, A. M and Chifiriuc, M. C. (2018). Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer. Frontiers in Immunology, 9

[2] Chassaing, B., Kumar, M., Baker, M. T., Singh, V. and Vijay-Kumar, M. (2014). Mammalian gut immunity. Biomedical journal37(5), 246–258.

[3] Ahluwalia, B., Magnusson, M. K. and Öhman, L. (2017). Mucosal immune system of the gastrointestinal tract: maintaining balance between the good and the bad. Scandinavian Journal of Gastroenterology, 52(11), 1185–1193.

[4] Walker W. A. (2017). The importance of appropriate initial bacterial colonization of the intestine in newborn, child, and adult health. Pediatric research82(3), 387–395.

[5] Hill CJ, Lynch DB, Murphy K, et al. (2017). Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort. Microbiome;5:4.

[6] Yang, I., Corwin, E. J., Brennan, P. A., Jordan, S., Murphy, J. R., & Dunlop, A. (2016). The Infant Microbiome. Nursing Research, 65(1), 76–88.

[7] Robertson, R et al.(2019) The Human Microbiome and Child Growth – First 1000 Days and Beyond. Trends in Microbiology. Vol. 27, No. 2

[9] Butler JE, Sun J, Weber P, Navarro P, Francis D. (2000) Antibody repertoire development in fetal and newborn piglets, III. Colonization of the gastrointestinal tract selectively diversifies the preimmune repertoire in mucosal lymphoid tissues. Immunology; 100: 119–30.

[10] Guarner, F., & Malagelada, J.-R. (2003). Gut flora in health and disease. The Lancet, 361(9356), 512–519.

[11]Hojsak, I. (2017). Probiotics in Children: What Is the Evidence? Pediatric Gastroenterology, Hepatology & Nutrition, 20(3), 139.

[12] Hojsak, I., Fabiano, V., Pop, T. L., Goulet, O., Zuccotti, G. V., Çokuğraş, F. C., Pettoello-Mantovani, M. and Kolaček, S. (2018). Guidance on the use of probiotics in clinical practice in children with selected clinical conditions and in specific vulnerable groups. Acta paediatrica (Oslo, Norway : 1992)107(6), 927–937.