How the infant gut develops: New study

Dr Kate Stephens PhD Food and Microbial Sciences; Gut Microbiology (University of Reading), BSc Medical Microbiology

We know that gut diversity in infants is important for helping babies to build up immune defences against common health issues, including digestive issuescolicallergieseczema and poor immunity. A recent study1, however, goes past the ‘why’ and has raised the question of ‘how’ the gut microbiota is developed to contain an array of diverse gut microorganisms, to support health and reduce the risk of future health problems.

So, what factors contribute to a new-born baby’s microbiome (head over to the Probiotics Learning Lab) development as they progress from infancy to childhood? And how long does this take to become established? Researchers at Baylor College of Medicine (Houston, USA) have discovered the answers to these questions in their latest paper. Published in Nature, the study explores the early journey towards a thriving and established gut microbiota (visit the Probiotics Learning Lab to find out more) and indicates how this foundation may help impact health in later life.

The study included 903 children in six locations across Europe and the U.S., aged from three to 46 months. The study analysed an enormous 12,005 stool samples from the infants. From this analysis, they found that there are three distinct phases in a child’s gut colonisation, starting from 3 months to 4 years of age. These include:

  • developmental phase (3-14 months)
  • transitional phase (15-30 months)
  • stable phase (31 months onwards)

So what lifestyle factors contributed to these crucial years of gut development?

breastfeeding mother

The main factors:


During the initial ‘developmental phase’, researchers found that breastfed or partially breastfed infants had significantly higher levels of Bifidobacterium, in particular Bifidobacterium breve & Bifodbacterium bifidum. As probiotic experts, we know all about this beneficial genus of bacteria and are very familiar with its benefits. There has been an increasing amount of evidence2, 3, 4, 5 highlighting the important of breastfeeding, as it contains crucial bioactive components for gut development such as prebiotics, immune factors, nutrients and beneficial microbes. To find out more about probiotics and breastfeeding, head over to the Probiotics Learning Lab.

Type of birth

Birth mode also significantly impacted the microbiome. Vaginal birth resulted in a temporary increase in Bacteroides, and this bacterial genus was associated with increasing gut diversity and maturation of the microbiome. Learn more with our blog on vaginal fluid swabbing for Caesarean babies over on the Probiotics Learning Lab.

The environment

Variants ranging from geographical location, to exposure to dogs (see Probiotics Learning Lab), also had an impact on microbial development and its symbiotic relationship with our immune system.

Moreover, these first phases of gut development are important not just during early life. Research is highlighting our microbial foundations may be associated with a range of potential diseases health issues in later life, including obesity, asthma and allergies. For more information on this, check out our Learning Lab for past studies on the importance of the gut microbiome in early life.

Also, it’s important to note that gut development doesn’t fully stop at 2.5 years of age - our microbiomes are constantly challenged throughout life from stimuli like antibiotics (head over to the Learning Lab to find out more), stress, and diet, to name a few. We are also seeing significant changes in our microbiomes as we reach the elderly life stage, with an overall decrease in diversity and a reduction in Bifidobacteria.

mother and baby touching noses

Now we know why - and more recently, how - good bacteria colonise in the gut, what can we do with this information? Senior author Joseph Petrosino said:

“[In this study] We showed that the first year of life is a key phase for the development of the microbiome, with the receipt of breast milk being the main factor that influences microbiome development over this period.”

However, as a result of certain mitigating circumstances, options for mothers such as breastfeeding and vaginal birth aren’t always possible. In lieu of these natural occurrences that contribute to an infant or child’s gut diversity, the good bacteria could be supplemented in the mother and baby to help support what would otherwise be missed. Furthermore, infants who were breastfed or vaginally birthed may also benefit, by boosting and maintaining their levels of friendly bacteria. This study highlights just how important our developmental stages are, and how fascinating the human microbiome is.

You may be interested in the following articles:

Probiotics lower risk of postnatal depression in recent study

Probiotics during pregnancy could reduce risk of childhood obesity

You might also like to read this blog, over in the Probiotics Learning Lab:

Microbirth: New film highlights importance of vaginal birth for babies’ microbiome

Or, find out more about probiotics.


  1. Stewart, C. J., et al. (2018). 'Temporal development of the gut microbiome in early childhood from the TEDDY study'. Nature, 562: 583–588
  2. Heikkila, M.P. and Saris, P.E., (2003). Inhibition of staphylococcus aureus by the commensal bacteria of human milk. Journal of Applied Microbiology. 95:471-478
  3. Bode, L., (2012). Human milk oligosaccharides; every baby needs a sugar mama. Glycobiology. 22 (9): 1147-1162
  4. Solis, G., et al., (2010). Establishment and development of lactic acid bacteria and bifidobacterial microbiota in breast milk and the infant gut. Anaerobe. 16 (3): 307-310
  5. Field, C., et al., (2005). The immunological components of human milk and their effect on immune development in infants. The Journal of Nutrition. 135 (1): 1-4