Fetuses are sterile in the womb, but beginning with the birth process, babies are exposed to microbes that originate from the mother and the surrounding environment including breast milk or baby formula. They tend 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.
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 baby. During cesarean deliveries, this transfer is completely absent. These babies commonly acquire and are colonized with flora from the hospital's environment and, therefore, their flora may differ from maternal flora. Babies delivered by cesarean section are colonized with more anaerobic bacteria, especially Bacteroides, than vaginally delivered babies. Clostridium perfringens is the anaerobic bacterium most frequently isolated after cesarean deliveries. When colonized, cesarean delivered babies less frequently harbor E. coli, and more often klebsiella and enterobacteria.
The initial colonizing bacteria vary with the food source of the baby. In breast-fed babies, 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 oligosaccharides (prebiotics), as well as production of lactic acid, cause an acid milieu and are the main reasons for its bifidogenic characteristics. In bottle-fed babies, Bifidobacteria are not predominant. 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 breast-feeding period.
Other factors affecting the intestinal microflora of the baby include geographical differences (industrialized vs. developing countries) and administration of antibiotics in neonatal intensive care.
L. gasseri and L. reuteri proved to be predominant indigenous Lactobacillus species in babies as well as in adults. Both species were occasionally present even in the stomach.
The bifidobacterial microflora differed in composition between babies and adults and in different stages of the host's life. Up to 5 species or special strains of bifidobacteria could be present in different, individually fixed, combinations.
Species typical for babies were B. bifidum, B. babyis, B. breve, and B. parvulorum.
Typical for adults were 4 different variants of B. adolescentis. B. bifidum and B. longum could often be found in both groups, but in lower numbers. B. longum showed some oxygen tolerance whereas B. bifidum and B. adolescentis required strict anaerobic and fastidious conditions for cultivation.
The lactobacillus species usually found in baby feces, Lactobacillus acidophilus, L. salivarius, and L. fermentum, are also present in adults.
All babies are initially colonized by large numbers of E. coli and streptococci. It has been proposed that these bacteria are responsible for the creation of an environment favorable for the establishment of the anaerobic genera Bacteroides, Bifidobacterium, and Clostridium. In breast-fed babies, reduction in numbers of E. Coli and streptococci, bacteroides, and clostridia then decrease in relation to dominance of Bifidobacterium.
The species of bidfidobacteria most frequently isolated and occurring in highest number was B. Breve in both breast-fed and formula-fed babies, with B. adolescentis, B. longum, and B. bifidum occurring less frequently and in lower numbers. Others report that B. babyis was dominant in breast-fed babies with B. longum and B. bifidum being the next most common.
After introduction of solid foods, obligate anaerobes increase in numbers and diversity until a pattern similar to that in adult humans is achieved by 2 years of age.
Oligosaccharides, including N-acetylglucosamine, glucose, galactose, and fucose oligomers or certain glycoproteins, which form a significant proportion of human breast milk, may be specific growth factors for Bifidobacterium.