A. Venn diagrams showing the overlap between genes affected by either SFB colonization of SW GF mice only (Group 2), introduction of Taconic microbiota into Jackson B6 mice by co-housing (Group 1), or both (Group 3). Total RNA was prepared from terminal ileum of the corresponding mice after 10 days of colonization and Affymetrix gene chip analysis was performed as described in Methods.
B. Heat-map analysis of the three groups in (A). Each line represents a single Affymetrix probe and each column a single mouse. Green, probes that were at least 2 fold down-regulated. Red, probes that were at least 2 fold up-regulated.
C. Top up-regulated genes in Group 3 in (A) arranged by fold change in GF+SFB mice.
D. Biological processes specifically induced by SFB (genes in Group 3 in (A)). Gene ontology analysis was performed as described in Methods.
E. Changes in anti-microbial peptide related genes upon SFB colonization and Th17 cell induction by co-housing. Each column represents an individual mouse.
F. RT-PCR analysis of selected genes, induced by SFB colonization. IQI GF mice (GF) were colonized with fecal homogenates from SFB-mono mice (SFB), Jackson B6 mice (Jackson), or a mixture of both (Jackson+SFB). Total RNA from terminal ileum was prepared 3 weeks later and RT-PCR performed as described in Methods.