From the way we’re birthed to the way we’re raised, the bacteria within our digestive system play a large role in our health. There are a number of protective measures humans have naturally developed over time to ensure that our offspring grow strong and healthy. Read on to learn how different bacteria cultures can affect our young ones.


Delivery Method

When babies are born, they have the same bacterial community throughout their entire body, whereas adults have several different bacterial communities in different locations throughout their bodies (e.g., mouth, skin, colon, and vagina). Authors of a study published in the journal, Proceedings of the National Academy of Sciences,1 analyzed bacterial cultures taken from the skin, vagina, and mouth of expectant mothers just before delivery and then analyzed and compared the bacterial cultures of the respective newborns’ skin. Babies born vaginally developed bacterial cultures similar to those in their mothers’ vagina, which were predominantly Lactobacillus whereas those who were born by C-section developed bacterial cultures similar to those on their mothers’ skin, which were predominantly Staphylococcus. The Lactobacillus strains help to protect the baby from many pathogens, including the Staphylococcus aureus strains that are resistant to all penicillins, commonly known as MRSA. The skin cultures do not offer these same benefits.

Other studies have shown that children born by C-section are more likely to develop asthma and allergies than those born vaginally and that giving C-section-born infants probiotics containing Lactobacillus from birth to 6 months of age reduces the risk of allergy at 5 years of age; however, probiotics made no difference in the vaginally-born children’s allergy risk.


Breast Milk

We know that human breast milk is beneficial for babies because it contains an ideal nutrient balance. New research shows it may also help newborns by nourishing specific beneficial intestinal bacteria unique to infants.

Human breast milk contains complex sugars known as human milk oligosaccharides (HMO). Although these comprise 21% of human milk, babies cannot digest them, and this has been baffling researchers for years, particularly since this milk composition is unique to humans.

A study published in Molecular Nutrition and Food Research,2 found that HMO is the perfect food (prebiotic) for a subspecies of Bifidobacterium longum bacteria to thrive, allowing it to grow strong and coat the baby’s intestinal wall, protecting it from harmful pathogens and helping the baby develop an efficient digestive system. This bacterium has an excessive number of genes associated with HMO metabolism, comprising >8% of its genome, making it the perfect bacteria to live in a breastfed human infant.3


Dietary Habits

A recent study published in the journal, Proceedings of the National Academy of Sciences,4 shows that dietary habits play a significant role in a child’s development of gut bacteria. Researchers analyzed and compared bacteria found in the stools of children 1-6 years of age from a developed European city and children from a rural African village. The diet of the African children was predominantly vegetarian, very high in fibre, and consisted mostly of cereals, legumes, and vegetables. The European children ate a typical Western diet containing little fibre and lots of animal protein, sugar, starch, and fat.

The results showed that the African children had beneficial gut bacteria that helped them break down fibres better, allowing them to extract more nutrition from fibre than could the European children. Beneficial bacteria in these children also seemed to help prevent the establishment of pathogens that can cause diarrhea, such as Shigella and Escheria. Bacteria present in the European children was less beneficial, setting them up for a higher likelihood of obesity later in life, and doing little to protect them from harmful pathogens.

The researchers suggest that this poor gut bacteria population results from insufficient fibre intake combined with little exposure to environmental bacteria, due to the excessive use of sanitation in the industrial world. Lack of beneficial gut bacteria could lead to a much higher risk of developing allergies, autoimmune disorders, and inflammatory bowel disease.



Making the best effort to exclusively breastfeed babies and then later raising them on a diet that is high in fibre and not too high in calories can be very beneficial for their gut flora, providing a good foundation for a healthy digestive system.

First published in the Inside Tract® newsletter issue 175 – 2010
1. Dominquez-Bello MG et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences. 2010;107:26:11971-5.
2. Ward RE et al. In Vitro fermentability of human milk oligosaccharides by several strains of bifidobacteria. Mol. Nutr. Food Res. 2007;51:1398-1405.
3. Schell MA et al. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proceedings of the National Academy of Sciences 2002;99:22:14422-14427.
4. De Filippo C et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences. 2010;107:33:14691-14696.