Fig. 5

Definition of persistent P. falciparum infection, incident P. falciparum infection, and incident febrile malaria. This longitudinal cohort study in Mali was designed to take advantage of the sharply demarcated 6-month malaria season (July – December) and 6-month dry season (January – June) during which there is either intense or negligible P. falciparum transmission, respectively. Stool microbiota composition was determined for all study subjects in a cross-sectional survey at the end of the 6-month dry season. For each subject, we examined the relationship between stool microbiota composition and the risk of persistent P. falciparum infection, incident P. falciparum infection and incident febrile malaria. Individuals with P. falciparum infections that persisted without symptoms through the dry season were identified by PCR analysis of fingerprick blood samples in a cross-sectional survey at the end of the 6-month dry season (at the time of stool collection). For subjects who began the malaria season without P. falciparum infection, incident P. falciparum infections during the ensuing malaria season were detected prospectively through bi-weekly PCR analysis of fingerprick blood samples. For all subjects who became infected with P. falciparum blood-stage parasites, incident cases of febrile malaria (axillary temperature ≥37.5 °C and ≥2500 asexual parasites/μl of blood) were detected prospectively during the ensuing malaria season through weekly physical examination by the study physician and blood smear microscopy if malaria was suspected