You inherit your first microbiome, the colony of bacteria that live in and on your body, from your mother at the moment you’re born. As scientists have started to decode the microbiome and understand its connection to many of the body’s systems including immunity and metabolism, they have learned that the type and concentration of bacteria in a baby’s microbiome varies depending on whether the baby was born via C-section or vaginal birth. In a recent experiment, scientists found that they could transfer a mother’s vaginal microbiome to a C-section baby cheaply and effectively using a swab of gauze, a technique called vaginal seeding. But according to an article published today in the British Medical Journal, that practice could be dangerous to the babies.

While the mother’s vagina contains a lot of bacteria that are good for a baby, it might also have some dangerous pathogens that the mother never even knew she had. The researchers mentioned B streptococcus, which is found in up to 30 percent of women and can cause an infection in the baby’s blood; as well as herpes virus and the bacteria that cause chlamydia and gonorrhea in adults and can bring on a nasty eye infection in newborns. Helping babies avoid those potential pathogens, which they’re exposed to during vaginal birth, is one of the advantages of a C-section.

In the swabbing experiment published earlier this month, the mothers were screened for just these sorts of microorganisms in order to be eligible for the experiment, which is not common practice for most pregnant women. Passing on the mother’s microbiome without that sort of test would put babies at risk of developing those sorts of infections, the study authors write.

The scientists behind the swabbing experiment admit that it will take years or decades until they know if vaginal seeding benefits babies in the long term. Until then, the researchers recommend that new moms don’t request the procedure at the hospital or do it themselves. And while the study authors write that doctors should respect the autonomy of mothers who do decide to do vaginal seeding, they also suggest that other practices, such as breastfeeding and limiting the use of antibiotics could have a much bigger effect on a baby’s microbiome without any of the additional risks.