Soil-transmitted helminths (STH) infect over a billion people worldwide, causing significant disease and sustaining poverty. As gastrointestinal pathogens, STH directly impact and are impacted by interactions with the microbial community of the host. These interactions likely play a role in the establishment, persistence, and infection load of STHs. Importantly, these interactions may play a role in the response of STH to drug treatment. Although there are an increasing number of studies focused on characterising human microbiomes, there is a significant underrepresentation of microbiomes from Africa relative to Western countries. Therefore, no existing datasets are suitable to address questions relevant to STH and host-microbiome interactions in STH-endemic countries. These data have been generated to assess the microbiome composition of human hosts infected or not with soil-transmitted helminths, and to understand if variation in the microbiome impacts treatment responses to anthelmintic treatment.