The GI microbiome influences dietary energy extraction, immune system development, vitamin production, and drug metabolism, yet most molecular and metabolic functions of the bacteria of the GI microbiome are uncharacterized [20
]. To gain insight into the functional consequences of IBD-associated dysbiosis, we used a novel approach pairing microbial community 16S gene sequence profiles with information from the closest available whole-genome sequences. This defined an inferred metagenome and thus complement of metabolic functional modules for each microbiome in this study. This allowed us to identify unique functional perturbations in the microbiomes of IBD patients. Interestingly, although we identified only nine changes in bacterial clades that associated with UC (of 350 total, 2.6%), we identified 21 statistically significant differences in functional pathways and metabolic modules (of 295, 7.1%); this pattern held for CD and iCD function as well. This underscores the fact that phylogenetically diverse changes in the composition of the GI microbiome can be functionally coordinated and lead to major modifications in the metabolic potential of the microbiota.
The microbial metabolic information available in this study represents only one step in the functional investigation of the IBD microbiota, as it is an accurate but approximate inference using prior knowledge of microbial genomes. The metagenomes inferred from our 16S data were supported by shotgun sequencing of a subset of samples, providing one confirmation that they were representative of community functional capability. As sequencing costs continue to fall, rich metagenomic data for dozens or hundreds of samples will further improve our ability to resolve species-level gene function in communities. Of course, a community expresses only a variable subset of its functional capability at any given time, in response to environmental stimuli. Thus, metatranscriptomic, proteomic, and metabolomic data will continue to add to our understanding of which of a community's potential functions are most strongly affecting the host during inflammatory disease.
Combining shifts in functional module abundance with prior knowledge of these metabolic pathways provides fresh insight into microbiome dysfunction in IBD. Metabolism of the sulfur-containing amino acid cysteine was increased in both UC and CD. This was accompanied by increases in riboflavin metabolism, glutathione transporters, and the N-acetylgalactosamine phosphotransferase system. Mucin, which is rich in cysteine and glycosylated sugars, is abundant in the intestinal epithelium, and it is upregulated during inflammation. The increases in cysteine metabolism and N-acetylgalactosamine transporters may reflect a shift in the microbiome towards greater abundance of microbes that use mucin as a primary energy source (Figure ). This functionality suggests activity at the mucosa and this may be problematic for a damaged IBD epithelium with compromised barrier function.
Figure 6 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 (more ...)
Alternatively, the increased biosynthesis of cysteine (a precursor of glutathione) and of glutathione transport modules may speak to the microbiome's response to the oxidative stress (high levels of reactive oxygen and nitrogen species) of the inflamed IBD gut [76
]. In support of this concept, we found that riboflavin metabolism, which is required to convert glutathione between its oxidized and reduced forms, is increased in iCD. Furthermore, the pentose phosphate pathway, which produces the NADPH also required for glutathione reduction, is increased as well. Recent studies have shown that redox stress allows Salmonella
to use ethanolamine as a carbon source [80
] and allows enterohemorrhagic E. coli
to use it as a nitrogen source [81
], thus conferring a competitive advantage to these microbes. This raises the interesting possibility that E. coli
or related species in IBD may be highly represented because they gain a competitive advantage from oxidative stress and are better able to compensate for it with glutathione production.
In both UC and CD, there were decreases in the biosynthesis of lysine, arginine, and histidine in favor of transport in both UC and CD; a further decrease in tryptophan metabolism was associated with iCD. The data showed additional broad decreases in many essential processes, such as cobalamin synthesis, purine and pyrimidine biosythesis, lipid catabolism, and phospholipid metabolism, as well as marked increases in transport. This overall decrease in abundance of genes for amino acid and nucleotide biosynthesis bears striking resemblance to the lifestyle of highly symbiotic bacteria that are intrinsically auxotropic and also of some pathobionts (Figure ). One such example are segmented filamentous bacteria (SFB), a symbiont that belongs to the Candidadatus
Arthromitis, a sub-group of clade I (sensu stricto
) Clostridia. A recently sequenced SFB genome lacked genes for nucleotide biosynthesis as well as nearly all vitamins and amino acids [82
]. SFB are often abundant in the rodent terminal ileum and are responsible for the maturation of Th17 cells [84
], which play an important role in CD-associated inflammation [85
]. To date, neither SFB nor phylogenetically related sequences have been observed in humans [82
]; this was also true in our data (zero 16S sequences with > 90% identity to X77814 SFB). However, a functional trend similar to SFB was observed in these IBD community metagenomes, as biosynthetic mechanisms throughout central carbon metabolism, amino acid biosynthesis, and nucleotide maintenance were all reduced (Figures and ), hinting that humans may host functional equivalents of SFB-like pathobionts that increase in IBD but are not phylogenetically close to Candidatus
Arthromitis. Host tissue destruction, either inflammation-mediated or bacterially mediated, would provide a ready nutrient source (Figure ).