The Global Enteric Multicenter Study (GEMS) investigated the cause, incidence and impact of moderate to severe diarrheal (MSD) disease in children. 514 MSD cases and 493 endemic controls from Bangladesh, The Gambia, Kenya and Mali were included. 1007 stool samples; V1-V2 region of 16S rRNA gene. Prospective, age-stratified, matched case-control design. Additional clinical and epidemiologic data for the same participants is available at ClinEpiDB.org.