Baby Microbiome: Nurturing Your Baby's Healthy Bacteria

By: Dr. Nazeli Gevorgyan - March 8, 2024 - 11 Minute Read

Baby Microbiome | The Milky Box

From birth, your baby’s microbiome plays a vital role in shaping their health and well-being, influencing many aspects, from digestion to immune function.

In this article, we’ll explore the science behind the baby microbiome and discuss how you can support your little one’s health by promoting a thriving microbial ecosystem from birth.

What is a Microbiome?

First, let’s understand what a microbiome is.

The human body harbors countless microorganisms, collectively known as the microbiota or microbiome, which work together with our cells to affect health throughout our lives, potentially impacting future generations. 

These organisms interact with our immune, hormonal, and nervous systems, with diverse populations residing on the skin, mouth, and gut.

What is a Microbiome? | The Milky Box

Your Baby’s Microbiome

Moms and kids share a special connection through their microbes, which starts early, with babies getting their first bacteria from their mom’s body. This early encounter shapes a friendly bacteria community that helps the child grow and develop.

During childbirth, the baby acquires bacteria from the mom's vaginal microbiota, which is primarily responsible for establishing the infant’s gut microbiome. The baby’s skin microbiota develops gradually through skin-to-skin contact immediately after birth, contact with caregivers, and exposure to the surrounding environment.

The Role of Gut Microbiome  

Starting from birth, the gut microbiota acts as a barrier against harmful organisms, helps break down food and drugs, makes vitamins, and helps absorb nutrients. It also supports the health of the intestines and keeps the immune system healthy. 

Gut Microbiome Role | The Milky Box

Gut Microbiome Development in Infancy 

In the first three years of life, babies initially have fewer types of gut bacteria compared to adults, but their diversity increases as they grow.

By around three years of age, the gut is fully colonized with a diverse range of microorganisms, which are in a balanced state. They can perform their roles effectively in this healthy state, contributing to overall well-being. However, if the gut is not colonized correctly, it can imbalance excellent and harmful bacteria, increasing the risk of health problems.

Therefore, babies must establish a healthy gut microbiota during this crucial period. Influential factors during this time include mode of delivery, antibiotic use, baby’s feeding practice, maternal health, and more.

Gut Microbiome Development in Infancy | The Milky Box

How Do You Build a Baby's Microbiome?

To promote a healthy microbiome in babies, focus on factors like promoting breastfeeding, encouraging skin-to-skin contact, introducing diverse nutritious foods, minimizing unnecessary antibiotic use, supporting maternal health, maintaining a clean environment, and more.

Let’s discuss these factors in more detail.

Nurturing Your Baby's Microbiome | The Milky Box

Aim for a Vaginal Birth

Choosing a vaginal birth, whenever possible, is not only a significant decision for the birthing process but also has important implications for the baby’s microbiome health. During a vaginal birth, babies are exposed to their mother’s vaginal and fecal microbiota, which sets the stage for a diverse and healthy gut microbiota.

This is significant because, generally, having a wide variety of microbes in the gut is seen as beneficial and promotes good health. On the other hand, babies born via cesarean section acquire bacteria primarily from skin surfaces and the birth environment, leading to less diversity and different types of bacteria.

Moreover, in instances where newborns are separated from their mothers after birth for an extended period, they might lose the chance for immediate colonization with the maternal skin microbiome.

While C-sections may be necessary in certain circumstances to ensure the safety of both the mother and the baby, you need to be aware of the potential differences in microbiome development.

Please note, that even though your baby was born by c-section, there are things that you can do to help your baby's microbiome. 

How Breastfeeding Sets the Pace of Baby Gut Development

Breastfeeding plays a crucial role in shaping the gut microbiome of infants, primarily through the transmission of beneficial probiotic bacteria that contribute to the colonization and maturation of the infant gut microbiome. Particular types of sugars facilitate this in breast milk, which act as prebiotics and promote the growth of these bacteria in the infant’s intestines.

Overall, breastfeeding is the best choice for infant nutrition. Not only are you giving your baby essential nutrients, but you’re also creating a solid foundation for their overall health and development. It’s a powerful way to bond with your little ones while giving them everything they need to thrive.

Encourage skin-to-skin contact

Skin-to-skin contact is essential for building a healthy microbiome in babies. Research shows that premature babies who experience skin-to-skin contact have different bacteria in their mouths and guts than those without. These specialized bacteria help improve intestinal function, the ability to digest food comfortably, and immune strength.

Holding your baby skin-to-skin right after birth and continuing to do so, along with exclusive breastfeeding, helps establish and nourish a healthy microbiome. If immediate skin-to-skin contact isn’t possible, start as soon as possible.

Skin to Skin | The Milky Box

Consider Vaginal Seeding

“Vaginal seeding”, a practice where doctors transfer some of the mother’s vaginal fluids to a baby born by cesarean section right after birth, aims to share the mom’s vaginal microbiome with the newborn.

Research by Song et al. suggests that restoring maternal microbes in cesarean-born babies helps their gut bacteria develop more like babies born vaginally.

Promote a Diverse Diet 

During infancy, milk-based feeding eventually becomes insufficient to meet the nutritional needs of babies. Hence, supplementation with additional foods alongside milk feeding, known as complementary feeding, is necessary. 

This transition typically occurs around six months of age, as recommended by the World Health Organization. The complementary feeding period coincides with significant changes in the gut microbiota species.

Introducing a diverse range of foods during this stage, including fruits, vegetables, cereals, meats, dairy products, and legumes, provides essential fiber and proteins that fuel the growth and diversity of gut microbes, ultimately contributing to a healthy and balanced microbiome.

Diverse Diet | The Milky Box

Consider Probiotics 

As previously discussed, breast milk contains pre- and probiotic components, which positively affect the gut microbiome.

If your baby is formula-fed, consider options fortified with prebiotics and probiotics. These have shown effectiveness in shaping the microbiota towards a breastfeeding-like pattern and boosting immune function.

Probiotics can also play a role in maternal health during pregnancy. Pregnant women, especially those who have used antibiotics or have disrupted microbiota, may benefit from probiotic supplementation to support a healthy vaginal microbiome, which can have implications for the infant’s early microbial colonization during birth.

Additionally, probiotic supplements designed specifically for infants can help promote a healthy gut microbiome in babies. Infants born via C-section or exposed to antibiotics face a higher risk of disruption of gut microbiota. A study was done to explore whether probiotic supplementation could mitigate these effects. 

A group of pregnant women and their infants received the same probiotics; the others didn’t. The adverse effects of antibiotics and birth mode were reduced or eliminated in the probiotic group, especially among breastfed babies.

Probiotics | The Milky Box

Probiotics in Baby Formula 

When selecting a baby formula, it is essential to consider the ingredients that can help promote the growth of a healthy microbiome in your baby's gut. Brands that contain probiotics and prebiotics are particularly beneficial in this regard, as they can support the development of beneficial bacteria that aid digestion and overall health.

These ingredients mimic breast milk's natural composition, which is rich in probiotics and prebiotics. By choosing a formula containing these components, you can help ensure your baby gets a healthy start to life.

HiPP Organic Baby Formula

HiPP Baby Formula is expertly crafted with the latest scientific research, providing a unique combination of prebiotics, probiotics, organic quality, and grass-fed protein in each container.

Additionally, each stage includes a distinctive blend of powdered organic milk, organic vegetable oils, and essential vitamins and minerals like folic acid, vitamin K, and vitamin C.

HiPP Baby Formula | The Milky Box

HiPP Dutch Organic Combiotic®

HiPP Dutch is a formula that is sourced and manufactured in Germany. It is then packaged in the Netherlands. The formula is made using organic skimmed milk from cows. 

HiPP Dutch Organic contains prebiotic fiber, which is derived from organic lactose. It is also enriched with lactobacillus fermentum hereditum® and natural probiotic lactic acid cultures.

HiPP Dutch Baby Formula | The Milky Box

HiPP German Organic Combiotic®

HiPP German formula offers easy-to-digest nutrition essential for your baby's growth and development. This organic formula contains prebiotics, such as galacto-oligosaccharides, and probiotics, such as organic lactic acid cultures, that aid digestion, promote healthy gut health, and boost immunity.

HiPP German Baby Formula | The Milky Box

Avoid Unnecessary Antibiotics 

Antibiotic use can have a significant impact on your baby’s developing microbiome. While antibiotics are essential for treating bacterial infections, they can also disrupt the balance of bacteria in your baby’s gut. 

Whenever antibiotics are necessary, it’s vital to follow your healthcare provider’s instructions carefully and consider measures to support the restoration of a healthy microbiome, such as probiotic use and a diverse diet rich in fiber and fermented foods. 

Antibiotics | The Milky Box

Baby Microbiome: Nurturing Your Baby's Healthy Bacteria

In conclusion, nurturing your baby’s healthy bacteria is crucial to their well-being. By understanding the microbiome’s importance and implementing practices like breastfeeding, skin-to-skin contact, good hygiene, mindful antibiotic use, diverse food introduction, and vaginal birth when possible, you can support the development of a robust and diverse microbiome for your little one.

At The Milky Box, we understand that every step you take to care for your baby's microbiome sets the stage for their long-term health and immunity. As a result, we provide organic formulas free of impurities and contain beneficial bacteria to support your bottle-feeding journey in the healthiest way possible.


1. Breastfeeding Skin-to-Skin Helps Baby Build a Healthy Immune System - La Leche League International. Available at:

2. Korpela, K. et al. (2018) ‘Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants’, Microbiome, 6(1), pp. 1–11. doi: 10.1186/S40168-018-0567-4/TABLES/1.

3. Korpela, K. and de Vos, W. M. (2022) ‘Infant gut microbiota restoration: state of the art’, Gut Microbes, 14(1). doi: 10.1080/19490976.2022.2118811.

4. Laursen, M. F. (2021) ‘Gut Microbiota Development: Influence of Diet from Infancy to Toddlerhood’, Annals of Nutrition and Metabolism, 77(Suppl. 3), pp. 21–34. doi: 10.1159/000517912.

5. Mueller, N. T. et al. (2015) ‘The infant microbiome development: mom matters’, Trends in molecular medicine, 21(2), p. 109. doi: 10.1016/J.MOLMED.2014.12.002.

6. Song, S. J. et al. (2021) ‘Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding’, Med, 2(8), pp. 951-964.e5. doi: 10.1016/J.MEDJ.2021.05.003.

7. Stojanović, N., Plećaš, D. and Plešinac, S. (2012) ‘Normal vaginal flora, disorders and application of probiotics in pregnancy’, Archives of gynecology and obstetrics, 286(2), pp. 325–332. doi: 10.1007/S00404-012-2293-7.

8. Yang, I. et al. (2016) ‘The Infant Microbiome: Implications for Infant Health and Neurocognitive Development’, Nursing research, 65(1), p. 76. doi: 10.1097/NNR.0000000000000133.

9. Yao, Y. et al. (2021) ‘The Role of Microbiota in Infant Health: From Early Life to Adulthood’, Frontiers in Immunology, 12, p. 708472. doi: 10.3389/FIMMU.2021.708472/BIBTEX.


Please be aware that this information is based on general trends in babies, and it is not medical advice. Your doctor should be your first source of information and advice when considering any changes to your child’s formula and when choosing your child’s formula. Always consult your pediatrician before making any decisions about your child’s diet or if you notice any changes in your child.

Breastfeeding is the best nutrition for your baby because breast milk provides your child with all the essential nutrients they need for growth and development. Please consult your pediatrician if your child requires supplemental feeding.

Nazeli Gevorgyan is a medical doctor from Armenia, and is a researcher in the fields of Obstetrics and Gynecology, among others. Dr. Nazeli is passionate with providing women and parents with reliable and high-quality information on healthy options for infant nutrition, breastfeeding, infant formula, and food. In her free time, she enjoys swimming, traveling, and pottery. 

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Reviewed by Suzanne Renee',

Infant Nutrition Expert

Suzanne Renee' is an accomplished professional with extensive expertise in the area of infant nutrition, dedicated to promoting the health and wellbeing of children. She started this journey as a foster parent.

Suzanne has emerged as a strong proponent of the European baby formula and has become a full-time writer on the subject. 

In her free time, she enjoys camping, hiking, and going to church.