When you think of picking up some bacterial germs, you would normally think that was a bad thing, especially in the labor and delivery room of a hospital. But a story on Fox News says new moms pass along a number of what is considered to be protective germs to their newborns as they pass through the birth canal, and babies that are delivered through C-Section may be falling behind on building their immunity.

At least, that appears to be the findings from a study by researchers which began at the University of Puerto Rico and is now underway at New York University (NYU). The new research suggests that doctors can pass along some of those missing microbes to the babies by swabbing them with their mother’s vaginal fluids within the first two minutes after delivery.

The samples size is small, comparing seven babies born vaginally with 11 C-section babies, including four who were swabbed with the mother’s bacteria. Over the period of the next month, the research team took samples from different parts of the infants’ bodies to monitor the development of the microbiomes in the children. More than 1,500 readings were taken during the study.

Those children who were swabbed with the fluids developed microbial neighborhoods more similar to those who were born vaginally than to the other C-section babies, according to microbiologist Maria Gloria Dominguez-Bello, who led the study.

Two types of bacterial species, Lactobacillus and Bacteroides, that are thought to play a major role in the development of the body’s immune system, were almost non-existent in the C-section babies that were not swabbed. Earlier studies have shown that C-section babies are at a higher risk of developing certain health conditions, such as asthma and allergies, so the new findings will likely lead to more research into whether the early development of the microbiome system plays a part in that development.

The study is continuing at NYU with 84 babies enrolled in the program, and they are having their microbiomes tested for a full year. Dominguez-Bello has already collected 13,000 samples, but lack of funding is causing a delay in the analysis.

Other scientists are cautioning that more research needs to be completed before the process can be considered, saying there are all sorts of bad bacteria that could be passed along as well. The simple message is we just don’t know enough to make an informed decision as yet.