The first 1000 days refer to your baby’s life from conception until they have reached 2 years of age. This is a critical time when your baby is still developing their gut microbiome, immune system, brain and other major organs. Nutritionally supporting the gut microbiome in early life can have lifelong health benefits.

The Gut Development in The First 1000 Days

During the first 1000 days of your baby’s gut development, your baby is establishing its microbiome diversity. The microbiota composition (variety and numbers of beneficial bacteria) fluctuates and follows a dynamic colonisation pattern. From approximately 3 years of age, your infant’s microbiota stabilises and continues to be relatively the same throughout their lifetime. However, as your child grows, diet, medications and lifestyle factors can alter the composition of their microbiome, potentially reducing the diversity and numbers of beneficial bacteria.

Three Distinctive Phases of Microbiome Development

  1. Developmental phase (3-14 months)
  2. Transitional phase (15-30 months)
  3. Stable phase (31-46) months

Studies have found that breastfeeding (exclusively or partially) was the most significant factor associated with microbiota composition during the developmental phase.

The Immune System Development in The First 1000 Days

As mentioned previously the gut and immune system develop rapidly throughout the first 1,000 days as babies move from a protected environment to one where they are exposed to lots of immune challenges. The development of your baby’s immune system begins in utero. In the last trimester, the mother starts to transfer antibodies via the placenta. Yet, their immune system is still incredibly immature at birth, as it has not been exposed to foreign antigens. Your baby’s immune system undergoes the most significant amount of change in the first year but continues to develop significantly until three. This process is sped up when older siblings are in the house or when infants attend childcare. It can feel like your baby is “forever unwell with a cold or flu”.

Nutrition plays a significant role in influencing the gut microbiota, shaping the development of both the gut and the immune system. Your baby’s gut health is essential for their developing immune system. This is because their immune system is housed in the gut. The gut and the immune system work synergistically to support one another to promote a healthy body. For instance, the gut microbiome acts as a gatekeeper and a trainer. It teaches immune cells called T-cells to distinguish foreign entities from our own tissue.

The Brain Development in The First 1000 Days

A baby’s brain develops more quickly during the first 1,000 days than any other moment in their lifetime. The way the brain moulds and adapts to its environment contributes to the person the baby will grow into. It also predetermines any risks for autism, ADD, ADHD, ability to concentrate and other behavioural issues. What is more, gut microbiota may also regulate brain development by producing bacterial metabolites, such as short-chain fatty acids (SCFA), and neurotransmitters such as γ-aminobutyric acid (GABA), serotonin and dopamine.

When babies are born, they are born with more neurons that they can use! Meaning they have more brain cells at birth than they will ever have again. As soon as they are born, neural connections between brain cells begin to happen. By age 3, neurons get wired to other neurons, forming about 100 trillion connections. How does the brain know what connections to make? Well, it depends on early interactions with their family members and surroundings. After the first three years, the brain begins to fine-tune itself. Connections used more often become more robust, while those not used are eventually eliminated. Building brain connections is like building muscles: you either use them or lose them.

Take action in helping your baby’s first 1000 days

  1. Support their gut health development, check out free eBook to find out ways on how to do this.
  2. Nourish their brain development with plenty of attachment parenting and healthy nutrients.
  3. Support healthy immune function by supporting their gut health and supplying plenty of nutritious foods.

Suspect your baby may have microbiome imbalances and an unhappy gut?

Download my FREE eBook to get a good understanding of what you can do for your baby’s gut health today.

Infant gut health ebook by Oh Healthy Baby


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).

Wang, S., Harvey, L., Martin, R., van der Beek, E. M., Knol, J., Cryan, J. F., & Renes, I. B. (2018). Targeting the gut microbiota to influence brain development and function in early life. Neuroscience & Biobehavioral Reviews, 95, 191–201.