By Sharon Lawton, Registered Nutritionist & Food Scientist
BSc (FSci & N), GCHN, RN
As a nutritionist - and more recently, as a mum to a very energetic toddler - I’ve always known the gut plays a major role in our health. Gut health starts far earlier than we might think – in fact, it begins before your baby even takes their first bite of food.
In this blog, I’ll walk you through why your baby’s microbiome matters from day one, and how you can support it with simple, everyday choices that lay the foundation for lifelong wellbeing.
What Is the Infant Microbiome?
The microbiome refers to the collection of microorganisms - bacteria, fungi, viruses, and other microbes - that live in and on the human body. In babies, this microbial community starts to establish itself during pregnancy, birth, and the first 1,000 days of life.
The gut microbiome, in particular, acts like a control centre for many essential functions:
• Digesting nutrients
• Training the immune system
• Protecting against harmful bacteria
• Supporting brain and cognitive development
Birth: The Microbial Milestone
Your baby’s mode of delivery significantly influences the first seeding of their microbiome.
• Vaginal birth: exposes the baby to beneficial bacteria from the birth canal, like Lactobacillus.
• C-section delivery: often results in different microbial exposures, primarily from skin and the hospital environment.
Although both delivery modes can lead to healthy outcomes, babies born vaginally often show earlier colonisation of gut-friendly microbes, which is linked to stronger immune development.
Breastfeeding and the Microbiome
Breast milk is a powerful contributor to a healthy infant microbiome. It contains:
• Prebiotics (like human milk oligosaccharides or HMOs) that feed good bacteria
• Probiotics (live beneficial bacteria) that help populate the baby’s gut
• Antibodies and enzymes that protect and support the immune system
Studies show that breastfed babies tend to have higher levels of Bifidobacteria, a group of bacteria strongly linked to gut and immune health.
Introducing Solids: A Critical Window
As babies transition to solids (typically around 6 months), their microbiome becomes more diverse. This is a golden opportunity to establish lifelong eating habits that support gut health.
Best first foods for gut health:
• High-fibre fruits and vegetables (like banana, avocado, pumpkin, pear)
• Whole grains (like oats, barley, or BARLEYMAX® Super Barley)
• Legumes (like lentils, chickpeas, black beans)
• Fermented foods (like plain yoghurt or kefir)
Diverse plant foods feed beneficial gut bacteria, helping to create a resilient and balanced microbiome.
Gut-Brain Connection Starts Early
Emerging research shows the gut is closely connected to the brain - often called the gut-brain axis. A healthy microbiome in infancy may influence:
• Emotional regulation
• Behaviour
• Cognitive development
In fact, disruptions to the infant microbiome (from antibiotics, poor diet, or environmental stress) have been linked to increased risks of allergies, asthma, obesity, and even mental health issues later in life.
How to Nurture Your Baby’s Gut Health
Here are simple, science-backed strategies:
1. Whilst birth plans do not always eventuate and delivery of baby safely is priority; if there is a choice, opt for vaginal birth to support natural microbial transfer.
2. As with birth plans, there may be obstacles to breastfeeding, but if you and baby enjoy the activity, primarily or wholly breastfeed to strengthen microbial growth.
3. Avoid unnecessary antibiotics in early life.
4. Offer a variety of plant-based, whole foods once solids are introduced.
5. Let them get dirty! Natural exposure to outdoor microbes helps diversify their microbiome.
6. Be mindful with sanitising – overuse of antibacterial products can reduce helpful microbial exposure.
A Healthy Gut for Life Starts Early
Your baby’s gut is more than just a digestive system - it’s a vital part of their foundation for lifelong health. By understanding the importance of the infant microbiome and making a few intentional choices, you can help set your little one up for better immunity, mood, digestion, and overall well-being.
Gut beginnings matter - and you’ve got the power to support them.
References:
• Benitez, AJ. et al (2025). Antibiotic Exposure is Associated with Minimal Gut Microbiome Perturbations in Healthy Term Infants. Microbiome.
• Fricker, AD. et al (2025). A Pilot Study Exploring the Relationship Between Milk Composition and Microbial Capacity in Breastfed Infants. Nutrients.
• Huang, H. et al (2024). Exposure to Prescribed Medications in Early Life and Impacts on Gut Microbiota and Disease Development. Clinical Medicine.
• Liu, T. et al (2025). Infant Gut Microbiota and Childhood Blood Pressure: Prospective Associations and the Modifying Role of Breastfeeding. Journal of the American Heart Association.
• Milani, C. et al. (2017). The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications. Cellular and Molecular Life Sciences.
• Pucci, N. et al (2025). Priority Effects, Nutrition and Milk Glycan-Metabolic Potential Drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome. PeerJ Publishing.
• Rodríguez, J. M. et al. (2015). The Composition of the Gut Microbiota throughout Life, with an Emphasis on Early Life. Microbial Ecology in Health and Disease.
• Vatanen, T. et al. (2018). The Human Gut Microbiome in Early Life: Implications for Health Outcomes. Nature Reviews Gastroenterology & Hepatology.
• Zhang, X. et al (2025). Association between fat-soluble vitamins in breast milk and neonatal gut microbiome in Tibetan mother-infant dyads during the first month postnatal. Food Research International.
