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.
General goal is to understand how dietary intervention might potentially be used to manage complex diseases. We aim to explore the effects of several common dietary components on intestinal microbiota and identity bacteria that affects host immune and metabolic parameters, with broad implications for human health.