The gut microbiome assembles in infancy and remains relatively stable until old age

The gut microbiome is established from birth and assembles in infancy, remains relatively stable and resilient during adulthood, and then declines in stability and function in older age.

Although it is recognized that the human gut microbiome changes as humans age, data on the structure and function of the gut microbiome in children is limited.

A wealth of studies have observed that gut microbiota diversity (the number of microorganism types and how they are distributed in the gut) converges towards an adult-like microbiota by the end of the first three to five years of life.

But gut microbiome science is not black and white and how the gut microbiome develops is still an unsolved puzzle.


The gut microbiome continues to develop beyond the first 3 years of life

Changes in gut microbiome composition have been noticed in pre-school (3-6 years) and school-aged children (ages 7-12 years). Although particular features of the gut microbiota in these age groups include an enrichment of beneficial Bifidobacterium and butyrate producers (e.g., Ruminococcus and Faecalibacterium species) and a reduction in archaea producing methane gas, overall there are no differences in microbial diversity between children and adults.

Another transition in gut microbiome composition is reported at 20 years of age. In a large group of 1,000 healthy Chinese individuals aged between 3 and more than 100 years old, scientists found that the major differences in the gut microbiome between groups of different ages were found in the 19 to 24-year-old group.

Interestingly, children under the age of 10 showed a richer fungal microbiota than adults, with unknown relevance for health outcomes.

The findings were driven by different demographics, breastfeeding duration, dietary fiber and plant-based protein, and lifestyle in the individuals under study. Before determining the duration of gut microbiome development, the findings should be replicated in other people from different countries. However, it seems microbiota development may take longer than previously thought.


What are the implications of the differences in gut microbiome composition between children and adults?

While we now have more information about changes at composition level, when translating that information for readers, it is also important to look at what these changes in gut microbes actually mean for children’s health.

Gut microbiome development represents a move towards higher bacterial diversity and functional complexity involving complex carbohydrate degradation, short-chain fatty acid synthesis and xenobiotic (drugs and environmental pollutants) metabolism, among others. Some authors found that the higher the plant-based diet intake, the better the metabolic response to glucose related to the high abundance of Bacteroides or Prevotella in the child’s gut.

Altogether, these microbiome functions support children’s ongoing development and reflect the diversity of substrates in the adult diet.

In a nutshell, recent studies suggest that gut microbiome development may take place more slowly than previously thought. Considering that diet is one of the most influential factors shaping the gut microbiome, the findings show that there is room for improving children and young adults’ diets to promote long-term health and prevent diseases.




Selma-Royo M, Tarrazó M, García-Mantrana I, et al. Shaping microbiota during the first 1000 days of life. Adv Exp Med Biol. 2019; 1125:3-24. doi: 10.1007/5584_2018_312.

Hollister EB, Riehle K, Luna RA, et al. Structure and function of the healthy pre-adolescent pediatric gut microbiome. Microbiome. 2015; 3:36. doi: 10.1186/s40168-015-0101-x.

Bian G, Gloor GB, Gong A, et al. The gut microbiota of healthy aged Chinese is similar to that of the healthy young. mSphere. 2017; 2(5):e00327-17. doi: 10.1128/mSphere.00327-17.

Zhong H, Penders J, Shi Z, et al. Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children. Microbiome. 2019; 7(1):2. doi: 10.1186/s40168-018-0608-z.

Derrien M, Alvarez AS, de Vos WM. The gut microbiota in the first decade of life. Trends Microbiol. 2019; 27(12):997-1010. doi: 10.1016/j.tim.2019.08.001.