4 μg/g mouse). See the Supplementary Materials for information on cell culture experiments, analysis of fecal samples by culture methods and quantitative polymerase chain reaction, isolation of DNA from fecal samples, preparation

of amplicon pool and 454-sequencing, bioinformatic analysis, isolation of lp dendritic (DC) and T cells, intracellular cytokine staining, flow cytometry, histology, and statistics. In a model of IBD, we investigated ICG-001 whether the endotoxicity of complex intestinal microbiota influenced the incidence or severity of colitis. Therefore, Rag1−/− mice, raised in a germ-free facility, were colonized with 2 types of complex intestinal microbiota with different endotoxicity. We used microbiota with a low TLR4-activating effect (Endolo) ( Figure 1A) characterized by low numbers of Enterobacteriaceae (including E coli) and high numbers of Bacteroidetes (including Bacteroides

vulgatus or Porphyromonas sp) ( Figure 1B and C) and, in addition, a high TLR4-activating microbiota (Endohi) ( Figure 1A) characterized by high numbers of Enterobacteriaceae and low numbers of Bacteroidetes as revealed by culture techniques ( Figure 1B) GSK-3 assay and quantitative polymerase chain reaction ( Figure 1C). Analysis of the intestinal microbiota by 454 sequencing of the 16S ribosomal DNA (rDNA) amplicons containing the variable regions V3−V6 revealed 70.3% of Bacteroidetes and 22.94% of Firmicutes in the EndoloRag1−/− mice. Proteobacterial (including E coli) 16S rDNA amplicons were below the detection limit. In EndohiRag1−/− mice, 0.19% of the analyzed 16S rDNA amplicons belonged to Proteobacteria (Enterobacteriaceae, including E coli, are a family within this phylum), 32.42% to Bacteroidetes and 61.84% to Firmicutes (including, eg, the classes Bacilli with the order of Bacillales and Lactobacillales, Clostridia, or Erysipelotrichia) ( Figure 1D). All mice described in this study were raised in these colonies to assure early perinatal colonization with the complex microbiota defined here. On transfer of T cells from healthy specific pathogen-free C57BL/6

mice the EndohiRag1−/− Cytidine deaminase mice developed severe colitis within 6 weeks, lost significant amounts of weight, and exhibited pronounced inflammation of colonic mucosa and submucosa. In contrast, T-cell−transferred EndoloRag1−/− mice remained healthy for 6 weeks, as indicated by both weight gain during the course of the experiment and missing histologic signs of inflammation ( Figure 2A−C). DCs in the colonic lamina propria (clp) of T-cell−transferred EndohiRag1−/− mice showed significantly higher expression of major histocompatibility complex (MHC) class II and CD40 as compared with the lp DC from EndoloRag1−/− mice ( Figure 2D). Intestinal inflammation was associated with a significant increase in CD4+CD3+ T cells in the clp as compared with healthy T-cell−transferred EndoloRag1−/− mice ( Figure 2E).