Proposed metabolic roles of the gut microbiome in IBD. Host-mediated processes (blue text) create an environment of oxidative stress in the intestine, which is more favorable to Enterobacteriaceae (increased abundance) than to clades IV and XIVa Clostridia (decreased abundance). This study's inferred IBD metagenomes include broadly increased oxidative metabolism, decreased SCFA production, and increased mucin degradation relative to healthy subjects. These processes all occur within microbes and rely on transport of small molecules to and from the lumen. The resulting tissue-destructive environment provides nutrients such as nucleotides and amino acids, which allow for increased growth of auxotrophic 'specialists'. Bacterial clades of interest are indicated in orange, bacterially mediated processes increased in IBD in red, and processes that decrease in green. Metabolic pathways differential in our IBD communities are contained in blue boxes. GSH and GSSG indicate reduced and oxidized forms of glutathione. LPS, lipopolysaccharide; NAG, N-acetyl galactosamine.