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The Baby Gut Microbiome

Jesse Jenkins

A new study has found that C-sections and formula-feeding disrupt the development of microbial communities in infants. How? Find out...

Cesarean sections (C-section) and strict formula-based feeding disrupt the development of microbial communities that promote lifelong health in an infant’s digestive tract, according to a new study by researchers at the University of Alberta.

C-sections and exclusively formula-feeding dirsupt the development of health gut micrbiomes in infants, according to a new study. Source: Wikipedia

In the study published in the Canadian Medical Association Journal (1), the researchers evaluated the composition of gut microbiomes of 24 4-month-old infants. When compared to vaginally delivered children, infants delivered by C-section were deficient in a specific genus of bacteria called bacteroides that helps breakdown complex molecules in the intestine.

“It’s known that C-Section delivery increases risks for allergies, asthma, diabetes and other chronic conditions,” said study author Anita Kozyrskyj, research chair at the Women’s and Children's Health Research Institute and associate professor in the Department of Pediatrics at the University of Alberta. “The goal of this research is to show how this might happen and whether it happens through changes in the gut microbiome in infants.”

In addition, the researchers found significant differences in the gut microbes of infants who were strictly formula-fed and those of infants who were breastfed. For example, formula-fed infants had an overrepresentation of Clostridium difficile bacteria, which has been associated with allergies and asthma.

To conduct the study, the team selected a subset of 24 infants from the large-scale Canadian Healthy Infant Longitudinal Development (CHILD) birth study of 3500 Canadian infants from four provinces. The subset was designed to represent the Canadian newborn population in which 25% of infants are born by C-section and 42% are breastfed at 4-months-old. The CHILD study data provided the group with the delivery information, maternal and infant diet data, previous environmental exposure information for the parents, and records of medications used during delivery.

Using high-throughput DNA sequencing, the team determined the microbial composition of the infants’ fecal samples. “Previously, gut bacteria could only be studied by growing, culturing them in the laboratory,” said study author Meghan Azad, a postdoctoral fellow at the Department of Pediatrics at University of Alberta. “The problem is, up to 90% of gut bacteria cannot be cultured in the lab; so until recently, we knew nothing about them.”

The first opportunity for infants to acquire bacteria is from the mother during vaginal delivery, but C-sections interfere with that process, according to Kozyrskyj. To further complicate the problem, mothers undergoing C-sections often receive a dose of prophylactic antibiotics to kill bacteria and reduce the risk of infection. Also, due to surgical complications, these mothers may be unable to breast-feed. “Those two additional factors, delaying breast feeding and the receiving of antibiotics, have the potential for keeping back the composition of the gut microbiome,” said Kozyrskyj.

Now, the team is working on better understanding the effects that these changes on the gut bacteria have on long-term health by expanding the study and increasing their sample size. “Our next goal is 200 infants, and we will finalize the data at 1 year of age, so this gives us more information about what happens during the first year,” said Kozyrskyj. “Eventually the goal is 2500 infants.”


1. Azad, M. B., T. Konya, H. Maughan, D. S. Guttman, C. J. Field, R. S. Chari, M. R. Sears, A. B. Becker, J. A. Scott, and A. L. Kozyrskyj. 2013. Gut microbiota of healthy canadian infants: profiles by mode of delivery and infant diet at 4 months. Canadian Medical Association Journal (February).