This study set out to define the consequence of diarrhea on maturation of the gut microbiome during the first 2 years of postnatal life. 271 children from the Amazonian lowlands near Iquitos, Peru 928 stool samples; V4 region of 16S rRNA gene. Prospective cohort design with samples obtained at postnatal months 6, 12, 18, and 24 Additional clinical and epidemiologic data for the same participants is available at ClinEpiDB.org.