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Background  In humans it is unknown if the composition of the gut microbiota alters the risk of  Plasmodium falciparum  infection or the risk of developing febrile malaria once  P. falciparum  infection is established. Here we collected stool samples from a cohort composed of 195 Malian children and adults just prior to an intense  P. falciparum  transmission season. We assayed these samples using massively parallel sequencing of the 16S ribosomal RNA gene to identify the composition of the gut bacterial communities in these individuals. During the ensuing 6-month  P. falciparum  transmission season we examined the relationship between the stool microbiota composition of individuals in this cohort and their prospective risk of both  P. falciparum  infection and febrile malaria.    Results  Consistent with prior studies, stool microbial diversity in the present cohort increased with age, although the overall microbiota profile was distinct from cohorts in other regions of Africa, Asia and North America. Age-adjusted Cox regression analysis revealed a significant association between microbiota composition and the prospective risk of  P. falciparum  infection; however, no relationship was observed between microbiota composition and the risk of developing febrile malaria once  P. falciparum  infection was established.    Conclusions  These findings underscore the diversity of gut microbiota across geographic regions, and suggest that strategic modulation of gut microbiota composition could decrease the risk of  P. falciparum  infection in malaria-endemic areas, potentially as an adjunct to partially effective malaria vaccines.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1819-3) contains supplementary material, which is available to authorized users.

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection