Recent studies have suggested that the intestinal microbiome plays an important role in modulating risk of several chronic diseases, including inflammatory bowel disease, obesity, type 2 diabetes, cardiovascular disease, and cancer. At the same time, it is now  understood that diet plays a significant role in shaping the microbiome, with experiments showing that dietary alterations can induce large, temporary microbial shifts within 24h. Given this association, there may be significant therapeutic utility in altering microbial  composition through diet. Studies have shown that consumption of particular types of food produces predictable shifts in existing host bacterial genera. Most of the studies profiled the microbiome using 16S rRNA amplicon sequencing, which utilizes the hypervariable  regions of the bacterial 16S rRNA gene to identify bacteria present in biological samples. However, 16S rRNA amplicon sequencing primarily provides information about microbial identity and not function. In order to investigate the microbiome’s functions,we have turned to a shotgun metagenomic approach in which the whole bacterial genome is sequenced. Despite a higher cost and more complicated bioinformatics requirement, shotgun metagenomics provides information about both microbial identity and gene composition.