MONDAY, Feb. 11 (HealthDay News) -- Being born by cesarean section has been tied to higher risks for various health problems in children, and now a new study finds these babies also have fewer "good" bacteria in their digestive tract.

Similarly, babies who were exclusively or even partially formula-fed rather than breast-fed also had markedly different gut flora than babies who were breast-fed, according to the study appearing in the Feb. 11 issue of the CMAJ (Canadian Medical Association Journal).

"Since other [researchers] have found associations between cesarean section delivery or formula-feeding and infant gut changes and conditions like allergy [and] asthma, we speculate that our observations may lead to poor health in later life," said study senior author Anita Kozyrskyj.

The findings support current clinical practice guidelines which favor vaginal delivery whenever possible, added Kozyrskyj, who is research chair and an associate professor of pediatrics at the University of Alberta, in Edmonton.

About a third of all U.S. births occur by C-section, a number considered by many to be far too high and potentially harmful to both the child and the mother.

Vaginal delivery, among other advantages, fosters the growth of trillions of good bacteria that reside peacefully in the human body (collectively know as a person's microbiome), many of them in the intestine.

Meanwhile, C-sections interfere with the newborn's exposure to bacteria in the vaginal tract, bacteria that essentially trains the immune system to react appropriately to future events, according to study background information.

Mothers who have C-sections also tend to start breast-feeding later and require antibiotics, both of which could also affect the baby's microbiome.

In the new study, researchers analyzed DNA from fecal samples taken from 24 healthy infants in four Canadian provinces at 4 months of age.

Compared with children who had been born vaginally, children who had been delivered by C-section had less diverse flora, lower levels of Shigellabacteria and none of the bacteria known as Bacteroidesat all.

" Shigellaand Bacteroidesare organisms picked up from mom and considered first colonizers," Kozyrskyj explained. "They lay the foundation for further microbes that become part of our normal microbiome."

Meanwhile, infants who were fed formula as opposed to breast milk also had less diverse flora and, in addition, had more of the bacteria Clostridium difficile, which had been associated with the development of allergies.

The study was a small one, but the researchers have collected fecal samples on 200 children and will be analyzing those in the future. They hope to eventually enroll 2,500 children in the study.

It's too soon to say definitively that the changes in the gut microbiome of children born by C-section will develop health problems. And it's possible that changes in the bacterial composition of the intestine as people age will compensate for diminished levels of bacteria in newborns, Kozyrskyj added.

A pediatric expert praised the new study.

"This is an important first step to make an association between intestinal bacteria and mode of delivery and type of feeding," said Dr. Michael Morowitz, a pediatric surgeon with Children's Hospital of Pittsburgh, at the University of Pittsburgh Medical Center.

Although follow-up studies will be needed, Morowitz added, "This is the latest piece of pretty convincing evidence that determinants very, very early in life can have an impact that lasts for months or years."

More information

Visit the U.S. National Institutes of Healthfor more on the Human Microbiome Project.