Human babies are colonized during passage through the birth canal by environmental microorganisms (for example, from the mother’s vagina or skin) and during breast feeding by microorganisms present in the milk137. Owing to the highly oxidative environment in the gastrointestinal tract of the newborn, primary colonizers are facultative anaerobic bacteria such as proteobacteria, which are thought to adjust the environmental conditions by decreasing the oxygen concentration to allow successive colonization by anaerobic microorganisms such as members of the genus Bacteroides and members of the phyla Actinobacteria and Firmicutes. During the first year of life, the intestinal microbiota composition is simple and fluctuates widely between individuals and over time. Microbial signatures stabilize and start to resemble the ‘adult
state’ when the infant reaches 1–2 years of age4. Interestingly, conflicting evidence has been published concerning the driving force for microbial transmission. In early studies of twins, the faecal microbial compositions in the mother and her children were similar, indicating a mainly maternal transmission108,111. However, in a more recent and extensive study, the same research group found that the faecal microbiota of children was no more similar to that of their mothers than to that of their biological fathers, and genetically unrelated but co‑habiting mothers and fathers were significantly more microbially similar to one another than to members of different families138. This indicates that, as well as genetics and kinship, environmental factors have a considerable effect on the microbial composition of the infant.