Figure 3.

Markers of inflammation are upregulated in the presence of old microbiota. Whole-genome gene expression in the ileum of mice (n = 5 per group) was assessed with Affymetrix GeneChip Mouse Gene 1.1 ST arrays. Genes that were significantly differentially expressed (P < 0.05 and fold-change >1.2) between young and old conventional mice, or germ-free (GF) recipients of young or old microbiota were analyzed with Ingenuity Pathway Analysis. (A) Canonical pathways that were most significantly affected by age or after transfer of aged microbiota. (B) Most significantly predicted upstream regulators by comparing young and old conventional mice, or GF recipients of young or old microbiota. (C) Venn diagram of differentially expressed genes between young and old conventional mice, and GF recipients of young or old microbiota.