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The phases of development of the gut microbiome in babies and children

Written by
Dr Fathalla Ali, PHD Paediatrics


In early life, the gut microbiota composition fluctuates and follows a dynamic and distinctive pattern of colonization. From approximately three years of age, a child’s microbiota becomes relatively stable and continues to be so throughout their lifetime. The first year of life is also characterized by the maturation of the immune system and there is evidence that the gut microbiota plays a vital role in the immune system development and potentially has a long-term impact on wellbeing and disease development during childhood. A group of researchers at Baylor College of Medicine in Texas investigated longitudinal 12,005 stool samples collected from 903 children between 3 and 46 months of age to understand the pattern of microbiota development in early years of life as part of The Environmental Determinant of Diabetics in the Young (TEDDY) study. The TEDDY study is a multi-centre study composed of Six clinical research centres: three in the USA (Colorado, Georgia/Florida and Washington), and three in Europe (Finland, Germany and Sweden).

The aims of the study were to :

  • “Study the pattern of gut microbiota development from 3 to 46 months of age.”
  • “Determine selected maternal and postnatal influences on the developing bacterial community during this same time period of early development.”
  • “Investigate the potential of the microbiome as a predictor for the development of Islet Autoimmunity (IA) or Type 1 Diabetes (T1D).”

Findings from this study found that:

  • Microbiota development during the first three years of life follows three distinctive phases of development:
    • Developmental phase (3–14 months): characterized by significant change in the diversity and 5 types of bacterial groups. Bifidobacteria Spp are the dominant microbiota during this phase.
    • Transitional phase (15–30 months): characterized by significant change the in diversity and 2 types of bacterial groups (Proteobacteria and Bacteroidetes).
    • Stable phase (31–46 months): characterized by high diversity and no change in bacterial groups. The dominant group of bacteria during this phase belongs to Firmicutes.
  • Breastfeeding (exclusive or partial) was the most significant factor associated with microbiota composition during the developmental phase.
  • Breastfeeding (exclusive or partial) was associated with the growth of Bifidobacterium. These bacteria exist viably in breast milk and have probiotic properties.
  • Cessation of breastfeeding but not the introduction of solid foods was associated with the maturation of the gut microbiota. This was marked by decrease in the abundance of Bifidobacteria Spp and increase in the abundance of Firmicutes.
  • Mode of delivery was also associated with microbiota development during developmental and transitional phases, driven by high abundance of Bacteroides Spp.
  • Living with siblings and furry pets were also associated with accelerating the maturation of gut microbiota.

In general, this study highlighted the importance of breastmilk on the maturation of gut microbiota during the first year of a baby’s life.


Stewart, C.J., Ajami, N.J., O’Brien, J.L. et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562, 583–588 (2018).

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