The First 1,000 Days of Life: The Link Between Nutrition & the Gut Microbiome

by Rebecca Williams, APD

The first 1,000 days of life, spanning conception to the age of two, are increasingly being recognised as a critical window where a child’s environment, including the impact of nutrition, can significantly influence their long-term risk of non-communicable disease. So much so that research suggests environmental factors in infancy may have a greater impact on disease risk than even genetics or environmental influences later in life(1).  Specifically gut microbial composition and early nutrition have been shown to play a critical role.

Gut microbial composition is unique to every individual and is thought to be strongly influenced by a number of environmental factors, including method of delivery (vaginal or Caesarean section), the mother’s diet, whether a child is breast or formula fed and also the time and method of introduction of solid foods(1). Breast fed infants, for example, are exposed to more than 700 species of bacteria through their mother’s milk, as well as a range of oligosaccharides (prebiotic fibres) which stimulate the growth of beneficial gut bacteria(2).

It’s been suggested that the establishment of the gut microbiome during the first 1,000 days is important for the development of ‘immune fitness’ and may result in a subsequent reduction of disease risk(1). The link between gut microbiota and health is influenced via short chain fatty acids such as butyrate and acetate – both produced when the gut microbiota ferment (or break down) the prebiotic fibres in our diets(4). Butyrate is thought to have anti-inflammatory effects, decrease rapid rates rates of cell reproduction and may have an ability to enhance the colonic immune response(6, 7) whilst also appearing to reduce intestinal pH which helps to prevent the growth of harmful bacteria(8).

In contrast, a reduction in the diversity and composition of gut microbiota in early life could result in an increased risk of developing non-communicable diseases in later life, including allergic diseases such as asthma, eczema and food allergies, autoimmune diseases such as multiple sclerosis, metabolic disorders including obesity and cardiovascular disease and other immune conditions such as inflammatory bowel disease(1).

A key life stage for infants which also has a significant influence on the colonisation and diversity of gut bacteria during infancy, is the introduction of solid foods:(3) foods that contain prebiotic fibres such as fructo-oligosaccharides, galacto-oligosaccharides and resistant starch support the growth and activity of beneficial gut bacteria(4). Demonstrating the link further, a recent Australian study found that infants could access the benefits of prebiotics at a younger age than previously thought, with babies as young as seven months showing increased microbial diversity following consumption of resistant starch from solid foods(5).

As outlined in the Infant Feeding Guidelines, solid foods should be introduced at around six months to meet an infant’s increasing nutritional and developmental needs. So in order to positively influence gut bacteria, it’s important to ensure they’re fed a balanced diet when beginning solid foods – introducing a variety of plant foods such as grains, legumes, fruit and vegetables as their first foods will ensure a varied intake of prebiotic fibres(9). It’s also important to ensure that the introduction of solid foods is complemented with an increase in water intake to prevent issues such as constipation, helping to promote good digestive health.

Emerging research demonstrates the importance of nutrition during the first 1,000 days of life, with this initial period increasingly being recognised as a key influencer for long-term health. Once established in this critical window, the composition of the gut microbiota remains relatively stable throughout our adulthood, but can be altered as a result of bacterial infections, antibiotic treatment and long-term dietary changes.

This evidence suggests that the establishment of a healthy and diverse gut microbiome is essential to promote immune health and reduce risk of chronic disease in later life not only during infancy, but also emphasises the critical role of nutrition on our gut microbiota as we move through all life stages.

To find out more on the benefits of grains and legumes throughout all life stages and for recipes and more, visit our website here.


  1. Tang M. Abstract: Role of Nutrition in Tolerance Development. Unpublished. 2016.
  2.  Rodríguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Juge N, et al. The Composition of the Gut Microbiota Throughout Life, with an Emphasis on Early Life. Microbial Ecology in Health and Disease. 2015;26:10.3402/mehd.v26.26050.
  3. Johnson CL, Versalovic J. The Human Microbiome and Its Potential Importance to Pediatrics. Pediatrics. 2012;129(5):950-60.
  4. Slavin J. Fiber and Prebiotics: Mechanisms and Health Benefits. Nutrients. 2013;5(4):1417-35.
  5. Gopalsamy GL, Christophersen CT, Bird AR, Young G. Abstract: Infants Can Ferment Resistant Starch Shortly After Wearning Which Changes Faecal Metabolite and Microbial Profiles. Unpublished. 2016.
  6. Bi Y, Qin N, Yang R. Human microbiota: a neglected “organ” in precision medicine. Infectious Diseases and Translational Medicine. 2015;1(2).
  7. Scott KP, Gratz SW, Sheridan PO, Flint HJ, Duncan SH. The influence of diet on the gut microbiota. Pharmacol Res. 2013;69(1):52-60.
  8. Flint HJ, Scott KP, Louis P, Duncan SH. The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol. 2012;9(10):577-89.
  9. Halmos EP, Christophersen CT, Bird AR, Shepherd SJ, Gibson PR, Muir JG. Diets that Differ in Their FODMAP Content Alter the Colonic Luminal Microenvironment. Gut. 2015;64(1):93-100.

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