INTESTINAL MICROFLORA IN THE NEWBORN INFANT
Fetuses are sterile in the womb, but beginning with the birth process, infants are exposed to microbes that originate from the mother and the surrounding environment including breast milk or formula(12). The infant tends to acquire the flora swallowed from the vaginal fluid at the time of delivery. Because vaginal flora and intestinal flora are similar, an infant's flora may closely mimic the intestinal flora of the mother(15).
Another factor affecting the intestinal flora of the newborn is delivery mode. A normal vaginal delivery commonly permits transfer of bacteria from the mother to the infant. During cesarean deliveries, this transfer is completely absent. These infants commonly acquire and are colonized with flora from the hospital's environment and, therefore, their flora may differ from maternal flora. Infants delivered by cesarean section are colonized with more anaerobic bacteria, especially Bacteroides, than vaginally delivered infants. Clostridium perfringens is the anaerobic bacterium most frequently isolated after cesarean deliveries. When colonized, cesarean delivered infants less frequently harbor E. coli, and more often klebsiella and enterobacteria(7). 
Above Figure: Factors shaping the neonatal microbiome. Maternal vaginal infections or periodontitis can result in bacteria invading the uterine environment. Gut and oral microbiota could be transported through the bloodstream from the mother to the fetus. Delivery mode shapes the initial bacterial inoculum of the newborn. Postnatal factors such as antibiotic use, diet (such as breast-feeding versus formula, and introduction of solid food), genetics of the infant and environmental exposure further configure the microbiome during early life. As diet diversifies with age, the microbiome gradually shifts toward an adult-like configuration, which is usually reached by age 3. Bacteria associated with the different processes are indicated.
Ref.: "The microbiome in early life: implications for health outcomes." Tamburini S, et all; Nat Med. 2016 Jul 7;22(7):713-22.
The initial colonizing bacteria vary with the food source of the infant. In breast-fed infants, Bifidobacteria account for more than 90% of the total intestinal bacteria. The low concentration of protein in human milk, the presence of specific anti-infective proteins such as immunoglobulin A, lactoferrin, lysozyme, and oligosacharides (prebiotics), as well as production of lactic acid, cause an acid milieu and are the main reasons for its bifidogenic charachtersitics. In bottle-fed infants, Bifidobacteria are not predominant(13). Instead enterobacteria and gram-negative organisms dominate because of a more alkaline milieu and the absence of the prebiotic modulatory factors present in breast milk.
The establishment of an intestinal microbial ecology is very variable at the beginning but will become a more stable system similar to the adult microflora by the end of the breastfeeding period.
Other factors affecting the intestinal microflora of the infant include geographical differences (industrialized vs. developing countries) and administration of antibiotics in neonatal intensive care.