Fig. 1

TIM-1 experimental set-up and analysis. The left side shows a picture of the TIM-1 system composed of four successive compartments simulating the human stomach and the three parts of the small intestine (i.e., the duodenum, jejunum and ileum) mimicking the main physicochemical parameters of human gastrointestinal digestion. Digestion experiments were performed to reproduce an adult or an infant (from 6 months old to 2 years old) ingesting a glass of water contaminated with 1 ×  108 oocysts of the C. parvum INRAE Nluc strain. On the right side, sampling times (minutes) are indicated when samples were taken either directly from each compartment (for flow cytometry, sporozoite luciferase activity and invasion assay); or indirectly by pooling the gastric effluents when the stomach compartment was solely used, or the ileal effluents when the entire TIM-1 system was used (for RNA sequencing). Digestions were run in triplicate. Created with BioRender.com (Agreement number: JH26ZFM4TU)