Study of microbial diversity in the midgut of Dredd mutant Drosophila, with or without PGRP-LE overexpression in enterocytes

This study is based on our observation that overexpression of the pattern recognition receptor (PRR) PGRP-LE in enterocytes acts independently of Relish/NF-kB signaling to alter metabolism in the midgut (the midgut is the equivalent of the small intestine in Drosophila). In contrast, Relish/NF-kB signaling is required to induce an innate immune response following stimulation of this PRR by bacterial cues. We sought to determine whether PRR-mediated metabolic remodeling of the midgut affects the composition of the microbiome. To test this possibility, we sequenced the V3-V4 hypervariable regions of the bacterial 16S rRNA gene in genomic DNA extracted from midguts. We performed these analyses in Dredd mutants with or without PGRP-LE overexpression in enterocytes. We used a Dredd mutant background because this mutation blocks the induction of Relish/NF-kB downstream of PGRP-LE, and thus the immune response. This genetic condition allows us to directly study the effect of PRR-mediated intestinal metabolic remodeling on midgut bacteria.