Strikingly, the number of differentially expressed genes between pIgR KO and WT mice was reduced to 27 when the conventional microbiota was suppressed by antibiotic treatment (Fig. 1A, red circle, and Supporting Information Table 2). We also compared gene expression between antibiotic-gavaged

pIgR KO and pIgR KO with a conventional intestinal microbiota and found 296 genes that were more than twofold differentially expressed (Fig. 1A, AZD0530 concentration yellow circle, and Supporting Information Table 3). Notably, 74 of the 208 genes differentially regulated between pIgR KO and WT mice with conventional microbiota were also regulated by antibiotic treatment (Fig. 1A, overlap between yellow and blue, and Supporting Information Table 4). To verify

the microarray results, we performed quantitative RT-PCR on several of the most up- or downregulated genes found within this overlap (Fig. 1B). We also verified by RT-PCR that AZD2281 concentration the mRNA encoding the xenobiotic-modifying enzymes, sulfotransferase family 1D member 1 (Sult1d1), and aldo-keto reductase family 1member 19 (Akr1c19) were downregulated in untreated pIgR KO (Fig. 1B). Interestingly, several AMPs were among the most upregulated in conventional pIgR KO compared with conventional WT colonic EC. Furthermore, expression of these genes was downregulated when the conventional microbiota was suppressed by administration of broad-spectrum antibiotics by gavage. To validate the microbiota-dependent differential expression of AMPs in pIgR KO and WT mice, we performed RT-PCR studies of several α-defensins (Supporting Information Fig. 1). These results confirmed the findings revealed Clomifene by microarray analysis. We found that colonic epithelial gene expression was altered in pIgR KO mice compared with WT mice and

hypothesized that this could be due to altered composition of the commensal microbiota between the two genotypes. To address this question, we analyzed the intestinal microbial communities in pIgR KO and WT mice by 16S rRNA gene-targeted phylogenetic microarray analyses. Total DNA was extracted from mouse cecum and fecal pellets from both genotypes of mice carrying conventional microbiota and subjected to mouse intestinal tract chip (MITChip) microarrays. This method can identify approximately 2000 operational taxonomic units (OTUs) characterized from mouse intestinal microbiota, and has recently been used to profile murine gut microbiota in different studies [25-28]. We first compared the microbial diversity of cecal and fecal samples from pIgR KO and WT mice and found a greater diversity in the cecal community in WT animals (Fig. 2A). Multivariate redundancy analysis (RDA) revealed that intestinal locations (feces, cecum) impacted the gut microbiota composition more than genotype (Fig. 2B).