Gut microbiome development continues between 6 and 9 years of age, with pre-school diet and breastfeeding acting as major driving forces

Besides diet, several other factors such as host genetics, ethnicity, age, medication, chronic diseases, physical exercise, stress, and sleep can all affect gut microbial composition. During the first 2 to 3 years of life, gut microbiota modulation appears to play a critical in later health outcomes. However, little is known about the impact of early lifestyle events on the gut microbiota of school-age children.

A new cohort study, led by Dr. Ilja Arts from the Maastricht University and Dr. Karsten Kristiansen from the University of Copenhagen (Denmark) and BGI-Shenzhen (China), reveals that breastfeeding duration and pre-school diet are major modulators of the gut microbiota of children aged between 6 and 9 years, with a connection between early diet and metabolic markers in their blood that showed enterotype dependency.

The researchers used shotgun metagenomics sequencing to analyze the fecal microbiota of 281 Dutch children of between 6 and 9 years of age, who are all part of the long-term KOALA Birth Cohort Study. The team also explored the relationship between the gut microbiome and environmental, biochemical and anthropometric parameters: early events (sex, type of delivery and feeding method), pre-school diet, blood parameters (glucose and branched-chain amino acids) and anthropometric measures (body mass index z-score and waist).

When compared with 62 age-matched healthy Dutch adults, the children showed an overall adult-like gut microbiota in terms of number of species and the proportion in which each species was represented in the community (within-group alpha-diversity), and of genus-based similarity (between-group beta diversity).

The enrichment of bacteria genera Bacteroides, Prevotella, and Bifidobacterium helped identify three main types of gut microbiota (called enterotypes) in children. Negative correlations were found between the abundance of species enriched in different enterotypes, whereas positive correlations were detected between species belonging to the same enterotype. Children with a high abundance of the genera Bacteroides had a more adult-like gut microbiome, whereas those with a high abundance of Bifidobacterium showed a much simpler structured gut microbiome.

No differences were reported in the relative abundance of gut microbiota species when overweight and lean children were compared. Furthermore, different microbial functional patterns relating to carbohydrate metabolism, amino acids and water- and lipid-soluble vitamin biosynthesis were detected between gut microbiome enterotypes.

Breastfeeding duration, the mother’s level of educational studies at the child’s birth, and pre-school dietary patterns explained the greatest variability in children’s gut microbial composition. When exploring associations between the gut microbiome and 45 early-life factors, the researchers found that children’s pre-school diet (including intake of plant-based protein and dietary fiber) and how long they were breastfed as infants correlated with the composition and functional capacity of the gut microbiota at 6 to 9 years of age.

It is worth mentioning that children’s early diet was linked to metabolic parameters in their blood—glucose, insulin and amino acid levels—which depended on the group of dominant bacteria to which the children belonged. Although the levels of blood metabolic parameters did not differ between the three enterotypes, the researchers found specific correlation patterns between children within each enterotype.

For instance, children within the Bacteroides and Prevotella groups showed an inverse correlation between high dietary fiber intake and low plasma insulin levels. In contrast, the children with a gut microbiome enriched in Bifidobacterium had a decreased microbial gene richness, gut microbiota richness (alpha-diversity), functional potential for complex carbohydrate fermentation and butyrate and succinate production.

In conclusion, these findings show how early-life breastfeeding duration and the pre-school diet play a role not only in gut microbiota composition and functional diversity, but also in the metabolic regulation of children at 6 to 9 years of age. Consequently, gut microbiota maturation is not complete by the end of the first three years of life and early-life factors have a relevant influence on gut microbiota in school-age children.



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.

GMFH Editing Team
GMFH Editing Team