The health of tiny humans may rely on the microbes they are exposed to within their first hours and years of life. Known as the ‘baby biome,’ this community of bacteria, fungi, and archaea plays a pivotal role in short and long term health. Many factors that shape the baby biome contribute to risk of health conditions like allergies, type 1 diabetes, and inflammatory bowel disease. How does the baby biome develop and where do these microbes come from?


Head, Shoulders, Knees, and Toes: Delivery Mode

Delivery mode is a major influencer of the composition and diversity of a baby’s microbiome. It is known that babies born via cesarean section have different microbial communities compared to babies born vaginally. During birth, the baby passes through the birth canal and is covered from head to toe in bacteria that originated from the mother’s vaginal canal. These beneficial microbes enter through the newborn’s nose and mouth and are the first to colonize the baby’s gut. On the other hand, c-section babies are first colonized by more harmful microbes typically found on hospital surfaces and the mother’s skin. C-section babies also have lower microbial diversity, which is a measure typically associated with increased risk of disease. Large observational studies have found associations between c-section births and increased risk of eczema, food allergies, asthma, type 1 diabetes, and obesity. However, these health outcomes are not definitive, and can be modified through other factors like nutrition and the environment.


The Very Hungry Caterpillar: Early Nutrition

The nutritional benefits of breastfeeding on an infant’s health and microbiome development are well established. Human breast milk contains proteins, hormones, and complex carbohydrates that develop the baby’s immune system, brain, and intestinal microbes. Although the nutritional content of baby formula is similar to human breast milk, formula-fed babies have different microbial communities compared to breast-fed babies. Prebiotics in breast milk produce short-chain fatty acids and vitamins, which strengthen the gut barrier and protect against infections. Breast milk also contains up to 104–106 bacterial cells per day, which have direct probiotic advantages for the infant gut microbiome. In addition, the mother’s skin has crucial  beneficial microbes that transfer to the infant during breastfeeding. For both breast-fed and formula-fed babies, timing of weaning and introduction to solid foods are important for transitioning a baby’s microbiome into an adult-like state. In addition to nutrition, environmental exposures are key to shaping the baby biome.


 Where the Wild Things Are: Environmental Factors

Environmental factors such as exposure to household pets and other animals, geographic location, and interaction with other children impact the microbiome from infancy into toddlerhood. Studies have shown that children with furry friends in the house, especially dogs and cats, have increased microbial diversity and lower rates of allergies compared to children with no pets.  Similarly, children exposed to farm animals also had protection against asthma, allergies, and inflammatory bowel disease. Geographic location was found to be a key environmental determinant of microbial communities that affect diabetes development in a study of over 900 children from Germany, Sweden, Finland, and three U.S. states. Finally, children who attend daycare within the first 2-3 years of life have a more mature microbiome compared to home care children, possibly due to greater interaction with diverse microbes from peers.


Baby biomes are influenced by many factors including mode of delivery, breastfeeding, complementary foods, geographic location, and exposure to animals and other children. Our understanding of baby biomes is still ongoing, but the impact of these findings on the future of babies, and their biomes, is bright.


Peer Editor: Runfan Yang

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