Initial acquisition of microbiota

Many of these microorganisms interact with the host in ways that are beneficial and often play an integral role in processes like digestion and immunity. The microbiome is dynamic: it varies between individuals, over time, and can influenced by both endogenous and exogenous forces.

Abundant research in invertebrates has shown that endosymbionts may be transmitted vertically to oocytes or externally transmitted during oviposition. Research on the acquisition of microbial communities in vertebrates is relatively sparse, but also suggests that vertical transmission may occur.

In humans

Early hypotheses assumed that human babies are born sterile and that any bacterial presence in the uterus would be harmful to the fetus. Some believed that both the womb and maternal milk were sterile, and that bacteria did not enter an infant's intestinal tract until supplementary food was provided. In 1900, the French pediatrician Henry Tissier isolated Bifidobacterium from the stool of healthy, breast-fed infants. He concluded that breast milk was not sterile and suggested that diarrhea caused by an imbalance of intestinal flora could be treated by supplementing food with Bifidobacterium. However, Tissier still claimed that the womb was sterile and that infants did not come into contact with bacteria until entering the birth canal.

Over the last few decades, research on the perinatal acquisition of microbiota in humans has expanded as a result of developments in DNA sequencing technology. Bacteria have been detected in umbilical cord blood, amniotic fluid, and fetal membranes of healthy, term babies. The meconium, an infant's first bowel movement of digested amniotic fluid, has also been shown to contain a diverse community of microbes. These microbial communities consist of genera commonly found in the mouth and intestines, which may be transmitted to the uterus via the blood stream, and in the vagina, which may ascend through the cervix.