Sup. Fig. 1 Sample set #1 WT mice (n = 3) Sample set #2

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Sup. Fig. 1 Sample set #1 WT mice (n = 3) Sample set #2 Histology LCM of microbes DNA extraction Histology LCM of microbes DNA extraction Histology LCM of microbes DNA extraction Pyrosequencing analysis Interfold region (29,560 reads) Digesta region (38,120 reads) Microbial density by quantitative PCR assays Interfold vs. digesta bacterial families: Bacteroidaceae* Enterococcaceae Lactobacillaceae Lachnospiraceae-Ruminococcaceae Random cloning and Sanger sequencing Interfold region (496 clones) Digesta region (377 clones) TRFLP and multivariate analysis Interfold vs. digesta Lachnospiraceae-Ruminococcaceae 16S rRNA gene classification and phylogenetic analysis Known type strains¥ Lachnospiraceae-Ruminococcaceae

Sup. Fig. 2 A B

Sup. Fig. 3 A B C

Sup. Fig. 4 Interfold Digesta Number of OTUs observed 97% 97% 95% 95% Number of OTUs observed 90% 90% 80% 80% Number of sequences