Variability and Stability of the Human Gut Microbiome

Abstract

During natural childbirth the gut of the newborn infant becomes colonized with microorganisms that come mainly from the mother, although they can also come from the environment. In non-natural (i.e. caesarean, as opposed to vaginal) births there is less opportunity for the normal, messy routes of inoculation via faecal material and body fluids and the early colonisers are more influenced by the skin surface and outside environment [1]. Which organisms become established during early life depends on the subsequent feeding regime, with breast feeding leading to different gut microbiota profiles compared with formula-based bottle feeding. In breast-fed infants, the faecal microbiota generally becomes dominated by bifidobacteria that compete most effectively for the human milk oligosaccharides (HMOs) produced in the mother’s milk [2]. In contrast, infants who are not breast-fed exhibit higher relative numbers of Firmicutes, Bacteroidetes and Proteobacteria and lower bifidobacteria [3]. The difference in gut microbiota composition between caesarian and naturally delivered babies is significant before 3 months of age, but begins to disappear thereafter [4, 5].