Caesarean births and feeding infants formula both shape which bacteria colonize our guts, according to a Canadian study into how those early changes could explain disease susceptibility later in life.

Gut bacteria help to digest food, stimulate the development of the immune system, regulate bowels and protect against infection. Doctors and scientists know less about how the microbes take hold early in life and what could disrupt the process.

How a newborn is born could affect what types of bacteria they acquire in their gut. (Michael Zamora/Corpus Christi Caller-Times/Associated Press)

In Monday's issue of the Canadian Medical Association Journal, researchers in Edmonton, Winnipeg, Toronto and Hamilton said they found infants born by caesarean delivery lacked a group of bacteria common in the stool of infants delivered vaginally, even if they were breastfed.

"Decisions regarding C-section delivery will influence the development of the infant's gut microbiome, with potential lifelong impact on health," study author Dr. Anita Kozyrskyj, of the University of Alberta said in an email.

It could be that C-section physically prevents newborns from acquiring microbes they would during vaginal births, Kozyrskyj said.

C. difficile bacteria that are associated with infections, allergy and asthma were overrepresented in infants fed formula.

"Infants born by caesarean delivery are at increased risk of asthma, obesity and Type 1 diabetes, whereas breastfeeding is variably protective against these and other disorders," researchers wrote.

"Our findings are particularly timely given the recent affirmation of the gut microbiota as a "super organ" with diverse roles in health and disease, and the increasing concern over rising cesarean delivery and insufficient exclusive breastfeeding in Canada."

Of the 24 infants delivered in Winnipeg in the study, a quarter were born by C-section, which reflects rates in Canada. In the study, 42 per cent of the babies were breastfed at four months of age. Less than 15 per cent of babies are exclusively breastfed as recommended for six months, previous national research suggests.

Elective C-sections

The comprehensive microbial survey was possible thanks to advances in DNA sequencing technology that allow researchers to examine the diversity of species in fecal samples taken when the infants were four months old.

The findings have important implications, Rob Knight of the departments of chemistry, biochemistry and computer science at the University of Colorado, Boulder, and his colleagues said in a journal commentary accompanying the study.

"These issues are of direct relevance to pregnant women and health practitioners and should be considered when choices such as elective caesarean delivery and other interventions are discussed," Knight said.

Breastfeeding did not correct the problems associated with C-section, said CBC Radio columnist Dr. Brian Goldman.

Goldman said the research will undoubtedly reignite existing controversies regarding C-sections and formula feeding. Given that it will take years to see if an infant born by C-section is at greater risk, he said there's no good reason to avoid having the discussion now as the authors suggest.

It's not yet clear what the ideal microbial makeup is or if different medicines or diets could change it, the journal commentators noted.

While researchers are planning a longer term study of more than 2,000 infants across Canada, they said they weren't able to detect differences by type of antibiotic, type of caesarean delivery or brand of formula in this study.

In caesarean deliveries, antibiotics are typically given on a prophylactic basis, so the factors are interrelated.

The study was funded by the Canadian Institutes of Health Research, AllerGen NCE, the Killam Trusts and Alberta Innovates Health Solutions.

With files from CBC's Amina Zafar