While we now appreciate the essential role of the microbiota as commensals and symbionts integral to immune [4] and metabolic [5] health, we are just beginning to understand how and when these microorganisms assemble and the early-life factors that disrupt their natural ecological succession. more than 100-fold and have such a broad influence on physiological regulation that they have been recognized as another organ [3]. Our previously limited view Amineptine of humanmicrobe interactions, strictly as pathogens causing Amineptine infectious diseases, has undergone rapid and dramatic expansion over the past two decades. While we now appreciate the essential role of the microbiota as commensals and symbionts integral to immune [4] and metabolic [5] health, we are just beginning to understand how and when these microorganisms assemble and the early-life factors that disrupt their natural ecological succession. Appreciation of the determinants and progression of the initial microbiome assemblage, particularly that of the gut (which is intimately involved in regulating our health), will afford insights into how the microbiome can be manipulated to improve health. The initial development and maturation of the neonatal microbiome is largely determined by maternaloffspring exchanges of microbiota. Disrupting the mother-to-newborn transmission of bacteria by C-section delivery may increase the risk of celiac disease [6, 7], asthma [811], type 1 diabetes [12, 13], and obesity [1416] in the offspring. Initial epidemiological evidence also indicates that disrupting microbial exchange through the use of antibiotics in pregnancy may increase offspring risk of childhood obesity [17] and asthma [18]. One study found that children exposed to prenatal antibiotics in the second or Amineptine third trimester had 84% higher risk of obesity compared with unexposed children [17]. In the same study, C-section was associated with 46% higher offspring risk of childhood obesity. After birth, breastfeeding introduces new microbial communities and stimulates the maturation of the neonatal gut microbiome [19, 20]. The use Amineptine of infant formula compared with breast milk has been found to impair the proper development of the neonatal immune system [21] and alter metabolism later in life [22]. While more research is needed to determine whether antibiotics, C-section delivery, and formula feeding are causally associated with autoimmune and metabolic diseases and, if so , the magnitude of these associations, the best available evidence suggests that these practices that compromise the microbial colonization of the newborn gut should be used prudently and followed by measures to restore the natural composition of the microbiome. Here we review the natural colonization and assembly of the neonatal microbiome, with particular focus on the gut, and the impacts exerted by antibiotics, C-section delivery, and formula feeding. We then discuss potential strategies for prevention and restoration of these microbiome insults. Lastly, throughout the review we indicate where further research regarding the acquisition, development, perturbation, and restoration of the neonatal microbiome is needed. == The maternal microbiome during pregnancy == Pregnancy affects all body systems, including the maternal microbiome. Gestational changes Amineptine in the vaginal [23, 24] and intestinal [25] microbiome are of particular relevance because these body sites are responsible for vertical microbial transmission to the newborn during vaginal delivery. The composition of CDC7L1 the vaginal microbiota changes throughout the course of pregnancy. In a cross-sectional study of 24 healthy gravid women at 1840 weeks of gestation, Aagaardet al. found that, compared with non-pregnant women, pregnant women had lower vaginal bacterial diversity, with dominance of lactobacilli, Clostridiales, Bacteroidales, and Actinomycetales [23]. Furthermore, specificLactobacillusspecies (L. iners, L. crispatus, L. jensenii, andL. johnsonii) had higher prevalence during later gestational ages [23]. A longitudinal study using sequence-based techniques analyzed vaginal samples serially collected from 22 non-pregnant and 32 pregnant participants. This study.