Diarrhoeal diseases are a major cause of childhood mortality in developing countries, yet in most cases no known pathogens can be identified by conventional diagnostic methods. Pop et al. used high throughput 16S rRNA sequencing to compare the faecal microbiota composition in 992 children from Gambia, Mali, Kenya and Bangladesh. This analysis established a strong association between diarrhoea and the presence of different organisms in the microbiota that had been previously associated with the disease, such as members of the Escherichia/Shigella genus and Campylobacter jejuni, and also revealed new associations, including bacteria from the genus Streptococcus and Granulicatella. By contrast, the presence of Prevotella copri and Lactobacillus ruminis correlated with protection from acute diarrhoea. Although person-to-person variability was high, the microbiota from children with diarrhoea was enriched in either facultatively anaerobic or microaerophilic bacteria and several obligate anaerobic bacterial lineages were present in healthy controls.