Volume 141, Issue 5, Pages 1773-1781 (November 2011) Bile Acid Is a Host Factor That Regulates the Composition of the Cecal Microbiota in Rats  K.B.M. Saiful Islam, Satoru Fukiya, Masahito Hagio, Nobuyuki Fujii, Satoshi Ishizuka, Tadasuke Ooka, Yoshitoshi Ogura, Tetsuya Hayashi, Atsushi Yokota  Gastroenterology  Volume 141, Issue 5, Pages 1773-1781 (November 2011) DOI: 10.1053/j.gastro.2011.07.046 Copyright © 2011 AGA Institute Terms and Conditions

Figure 1 Effect of CA feeding on bile acid and organic acid compositions in rats of different diet groups. (A) Major bile acids found in feces. For the control and H-CA groups, n = 12; for the M-CA group, n = 9. (B) Major organic acids found in the cecal contents. For the control and H-CA groups, n = 6; for the M-CA group, n = 9. Total SCFAs are the sum of acetate, propionate, and n-butyrate. Total organic acids are the sum of all the organic acids detected. The mean ± SEM was plotted. Different lowercase letters indicate significant differences in each acid (P < .05; Tukey–Kramer test). Gastroenterology 2011 141, 1773-1781DOI: (10.1053/j.gastro.2011.07.046) Copyright © 2011 AGA Institute Terms and Conditions

Figure 2 Effect of CA on bacterial morphology in rat cecal contents and total cell count as revealed by DAPI staining. (A) Control group, (B) M-CA group, and (C) H-CA group. Values for the total cell count per gram wet cecal content are given as the mean ± SEM. The values labeled with different lowercase letters are significantly different (n = 6 for the control and H-CA groups, and n = 9 for the M-CA group, P < .05; Tukey–Kramer test). Gastroenterology 2011 141, 1773-1781DOI: (10.1053/j.gastro.2011.07.046) Copyright © 2011 AGA Institute Terms and Conditions

Figure 3 Composition of cecal microbiota of rats from different diet groups as revealed by sequencing of 16S rRNA gene clone libraries. Population analyses for each diet group included (A) phyla, (B) classes, and (C) major genera found. Mean percentage (%) of the total population is shown (n = 6 for each diet group). Classification is based on a 95% confidence threshold using a total of 825 sequence reads (control group = 266 reads, M-CA group = 274 reads, and H-CA group = 285 reads). “Unclassified” means bacteria not able to be classified by the RDP pipeline. See Supplementary Tables 8 and 9 for detailed distribution of bacteria by different diet groups. Gastroenterology 2011 141, 1773-1781DOI: (10.1053/j.gastro.2011.07.046) Copyright © 2011 AGA Institute Terms and Conditions

Figure 4 Analysis of microbiota in rat cecal contents by FISH using the Eub338, Erec482, and Bac719 probes. The mean ± SEM was plotted for each group. Different lowercase letters represent significant differences (n = 6 for each diet group, P < .05; Tukey–Kramer test). Gastroenterology 2011 141, 1773-1781DOI: (10.1053/j.gastro.2011.07.046) Copyright © 2011 AGA Institute Terms and Conditions

Figure 5 OTU analysis of rat cecal microbiota populations from different diet groups. OTUs are indicated by numbers. OTUs that comprise at least 4 sequences are displayed. Total sequence reads used for OTU analysis was 845 (control group, 276 reads; M-CA group, 279 reads; H-CA group, 290 reads). O-Fir, the other Firmicutes; O-Bac, the other Bacteroidetes; O-Pb, the other Proteobacteria; O-Ab, the other Actinobacteria. OTUs consisting of 1 to 3 sequences are combined into O-Fir, O-Bac, O-Pb, and O-Ab. Gastroenterology 2011 141, 1773-1781DOI: (10.1053/j.gastro.2011.07.046) Copyright © 2011 AGA Institute Terms and Conditions