Anopheles stephensi immune factor APL1 confers specific protective tolerance to an otherwise lethal enteric microbiome clade

The commensal gut microbiome is contained and controlled by the enteric epithelial barrier, but little is known about the specificity of host immune barrier interactions with gut commensals. Here, we show that depletion of APL1 in the Asian malaria mosquito Anopheles stephensi causes elevated mortality and higher midgut abundance of a clade of Enterobacteriaceae. Microbiome-wide association mapping for the APL1-dependent mortality phenotype highlights just two operational taxonomic units belonging to Klebsiella and Cedecea genera. Antibiotic treatment complements the loss of APL1 function, reversing the dysbiosis as well as mortality. Thus, APL1 activity is essential for A. stephensi survival, and appears to confer specific protective tolerance to maintain the commensal state of an otherwise lethal clade within the enteric microbiome. Successful Plasmodium development in A. stephensi also depends upon APL1 activity for protection from high host mortality, probably caused by bacterial penetration during parasite invasion of the midgut. Phylogenomic analysis indicates that APL1 is present as a single ancestral gene in most Anopheles including A. stephensi, but expanded to three paralogs in an African lineage that includes only the Gambiae species complex and Anopheles christyi. Silencing of all three APL1 paralogs in A. coluzzii does not result in elevated mortality, either with or without Plasmodium. The decoupling of commensal bacterial tolerance and Plasmodium infection success could be a factor contributing to the exceptional levels of malaria transmission mediated by human-feeding members of the Gambiae complex in Africa.