Paneth cell α-defensins are antimicrobial peptides involved in the control of the intestinal microbiota and immunological homeostasis. In mice, they are encoded by multiple, highly homologous genes <i>(Defa)</i>. The transcriptional activity of ileal <i>Defa</i> genes was studied in response to pharmacological and genetic perturbations of the intestinal environment of C57BL/6 mice. <i>Defa</i> gene transcription was sensitive to oral antibiotic administration suggesting that commensal microbes regulate <i>Defa</i> expression. Ileal microbiota analysis showed that decreased transcription of <i>Defa</i> genes correlated with depletion of <i>Lactobacillus</i>. <i>Defa</i> expression was partially restored in vivo by lactobacillus administration to antibiotic-treated mice. <i>Defa</i> transcripts were less abundant in ex vivo, microbiota-free intestinal explants but recovered after explant exposure to UV-killed bacteria, Toll-like receptor (TLR)-2 or TLR4 agonists. Genetic deficiency of several TLRs or MyD88 led to dramatic drops in <i>Defa</i> transcription in vivo. These results show that Paneth cell <i>Defa</i> genes are regulated by commensal bacteria through TLR-MyD88 signaling and provide a further understanding of the dysregulation of intestinal homeostasis that occurs as a result of imbalances in the populations of commensal bacteria
