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Babies born vaginally are colonized by microbes from the mother’s birth canal. Many of these microbes are beneficial (such as Lactobacillus which helps digest milk), whereas babies born by Caesarian delivery are colonized by environmental bacteria present in the hospital which can include some pathogens. Some experts believe the difference in microbial exposure based on delivery method could have life-long health impacts.

A study published in 2015 found that four key microbes in babies’ guts had a strong negative correlation with asthma development (i.e. when these four microbes were present the risk of asthma was greatly reduced).

http://www.npr.org/sections/health-shots/2015/09/30/444746094/missing-microbes-provide-clues-about-asthma-risk

Researchers believe microbial exposure during delivery can have implications in the development of certain autoimmune and metabolic disorders such as Type 1 diabetes, allergies, obesity, asthma, Chrohn’s disease, thyroid issues and sinus problems.

A study released recently found that babies born via Caesarian delivery can be intentionally exposed to the mother’s beneficial bacteria to overcome the microbial concerns about C-section delivery. This method involves collecting a mother’s vaginal fluids prior to surgery using a swab and wiping all of the infant after birth for a couple minutes to inoculate. These findings are critical as the rate of C-sections is now 1 in 3 births and rising and the rate of autoimmune and metabolic disorders has also been rising.

https://www.bostonglobe.com/news/nation/2016/02/01/post-caesarean-bacteria-transfer-could-change-health-for-life-study-shows/gVmXx9L4jJzrjCpoE20pWN/story.html

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110651/