Longitudinal study of children gut microbiota up to 5 years of age

The gut is inhabited by a densely populated ecosystem, the gut microbiota, that is established at birth. However, the succession by which different bacteria are incorporated into the gut microbiota is still relatively unknown. Here, we analyzed the microbiota using 16S rRNA gene profiling from 471 children followed from birth to 5 years of age, sampled at 4 and 12 months and after 3 and 5 years as well as their mothers at birth. We also compared their microbiota to an adult Swedish normal population. Bacterial genera followed 4 different colonization patterns during establishment. We also identified genera which colonized late, such as Methanobrevibacter and Christensenellaceae. These late colonizers correlated with increased alpha diversity in both children and adults. By following the children through age specific community types, we found that the gut microbiota had individual dynamics and trajectories. Although, birth through c-section had large effects on the gut microbiota in infancy we did not observe any clear effects of c-section on the gut microbiota development after 1 year of age.