The type of birth delivery (vaginal birth or Caesarean section) and infant feeding practices (breastfeeding or formula-feeding) may have a direct impact on the maturation of the infant’s gut flora. This can in turn have potentially lifelong health repercussions on the newborn.

Importance of the human microbiome

The human microbiome or microbiota refers to the trillions of microbes harboured by the human body with the digestive tract containing the highest density of bacteria — a minimum of 10 microbes to 1 host cell.

These gut bacteria play an indispensable role in human health: they stimulate the development of the immune system, offer protection against harmful organisms, maintain a healthy intestinal environment and are involved in nutrient processing as well as the body’s efficient use and storage of energy.

The authors write that “the disruption of the gut microbiota has been linked to an increasing number of diseases, including inflammatory bowel disease, necrotising enterocolitis, diabetes, obesity, cancer, allergies and asthma.”

Determinants of the gut microbiome during infancy

Several factors influence the newborn’s gut microbiome but breastfeeding and mode of delivery are the two most extensively researched determinants.

During a Caesarean delivery, the infant is not exposed to the mother’s microbes — this hinders normal colonisation of the infant’s gut, making the newborn more susceptible to asthma, obesity and type 1 diabetes later in life.

On the other hand, breastfeeding can protect against these and other disorders since the mother’s milk promotes the development of a healthy gut by providing “food” for the beneficial bacteria.

Study details

A team of Canadian researchers conducted this study to better understand the acquisition of the human microbiome during infancy and what may impede the growth of these friendly bacteria. They analysed data from 24 healthy term infants who participated in the Canadian Healthy Infant Longitudinal Development (CHILD) study which involved 3,500 newborns from 4 provinces.

Stools samples were collected from the infants at age 3 to 4 months and analysed using a new technology involving culture-independent DNA sequencing. Compared to traditional laboratory cultures which cannot grow about 80% of intestinal microbes, this technique enables the detection of almost any bacteria as it does not rely on laboratory cultures at all.

The mothers also completed a questionnaire regarding the infant’s diet which was categorised as exclusive, partial or no breastfeeding.

Study highlights

The researchers reported a significantly smaller bacterial community among infants who were born via Caesarean delivery compared to those who were given birth vaginally. Moreover, a specific group of bacteria remained undetected among the Caesarean section babies, including those who were breastfed.

Infants born by elective Caesarean delivery had a lower bacterial diversity and richness compared to those born by emergency Caesarean delivery. The researchers stated that “further research is warranted to determine whether these differences are related to feeding, antibiotics or perhaps “partial” microbial exposure during emergency caesarean delivery following membrane rupture.”

The gut bacteria of strictly formula-fed babies was also considerably different from that of exclusively or partially breastfed infants. A significantly higher proportion of C.difficile, a pathogen tied to intestinal diseases and hypersensitivity reactions, was detected among infants not receiving any breast milk compared to those who were breastfed.

This peer-reviewed study was published in CMAJ (Canadian Medical Association Journal).


    Azad et al (2013) Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. CMAJ. 185(5):385-94.