Mode of Delivery to the Brave New (Microbial) World: A Defining Moment for the Respiratory Microbiome?

The index event of birth has always been viewed as the most challenging physiologic adaptation of our lives. With the emergence of microbiome science, we have appreciated yet another critical transition that occurs at birth: the fetus exits the sterile (or at least low in microbial biomass (Funkhouser and Bordenstein, 2013)) environment of the womb to enter the outer world ecosystem with abundant microorganisms. This route of entry to the microbial world, or mode of delivery, can determine which of the mother's microbes have the first shot at founding colonies within the baby's body. Vaginal birth offers a prolonged exposure to vaginal and intestinal microbiota, whereas Caesarian section (C-section) directly exposes the fetus to skin and environmental microbes (Dominguez-Bello et al. 2010). As the seeds of the developing infantile microbiome are planted at birth, the well-established downstream associations of C-section with childhood respiratory illness, such as asthma and respiratory infections (Black et al. 2015), may in fact reflect the effects of C-section on microbiota. With extensive evidence linking specific profiles of the respiratory microbiome of children with subsequent development of respiratory illnesses (Lynch and Boushey, 2016), Bosch et al. (2016) in this issue of EBioMedicine examine a logically emerging hypothesis: does C-section impact the evolution of the upper respiratory microbiome? In this well-designed birth cohort study, the investigators prospectively followed 102 neonates born either vaginally or by C-section and repeatedly sampled their nasopharyngeal microbiome at regular intervals up to six months of age. Immediately after birth, the nasopharynx of babies was coated by a low biomass bacterial community of mixed origin, with species of presumed fecal and vaginal origin being more common in vaginally-delivered neonates. Following an outgrowth of Streptococcus viridans by 24 h after birth, neonates developed individual