A child’s microflora is closely linked to the method of delivery. The microbiome of the very first days of life develops and impacts health throughout a person’s life. During vaginal delivery, the baby comes in close contact with the mother’s vaginal and intestinal microflora. These bacteria then spawn the first bacterial colonies in the baby’s body. Babies, that for objective reasons are born via Cesarean delivery, do not get this close contact with the mother’s microflora, therefore the first bacteria to enter their bodies are bacteria from the outside world, i.e. the operating room. 
The microflora content acquired in the first days of life may have a long-term impact on the intestines of breast-fed babies. For example, one study found that the intestinal flora in babies born via Cesarean delivery was disrupted even 6 months after birth. Another study indicated the intestinal microflora in babies born via vaginal delivery and Cesarean differed even at the age of 7.  There are conclusive results that the intestinal microflora affects the development of a child’s immune system. Since it is clear that the microflora of babies delivered by Cesarean differs from that of babies delivered naturally, the development of their immune systems will also thus be different. Available studies show that Cesarean babies are more prone to atopic diseases, such as asthma, allergic rhinitis and atopic dermatitis. Furthermore, they also show higher susceptibility to celiac disease, type 1 diabetes and more frequent diarrhea. 
- Neu J, Rushing J. Cesarean versus vaginal delivery: long-term infant outcomes and the hygiene hypothesis. Clin Perinatol. 2011 Jun;38(2):321-31
- Grönlund MM, Lehtonen OP, Eerola E, et al. Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery. J Pediatr Gastroenterol Nutr. 1999; 28(1):19–25.
- Salminen S, Gibson GR, McCartney AL, et al. Influence of mode of delivery on gut microbiota composition in seven year old children. Gut. 2004; 53(9):1388–9.