The role of the gut microbiome in host health is becoming clearer with better characterisation of the nutritional, biochemical and immunological function of the microbes. However, to date, there is a paucity of studies describing/ investigating the role of the gut microbiome in infection, pathology and acquired immunity in children exposed to helminths, in sub-Saharan Africa. We determined how the diversity and abundance of different gut bacteria taxonomic groups differ with age, sex and infection with the helminths parasites causing bilharzia/schistosomiasis in children aged 6 months -13 years. The parasites are controlled by treatment with the antihelminthic praziquantel (PZQ), which is associated with diarrhoea within the first 24 hours of treatment in some children. We therefore also investigated the effects of PZQ treatment on the gut microbiome of the children 12 weeks post-PZQ treatment. The composition of the gut microbiome changed with age within the 0–3 year age range and also differed significantly in abundance of the different taxonomic groups between infected and uninfected children prior to treatment with PZQ. However, the pre-treatment microbiome structure was not altered by antihelminthic treatment of infected or uninfected children. Further studies are required to investigate causality and mechanisms of interaction.