Humans act as a host to trillions of microorganisms. The collective of these microorganisms is called a host’s microbiota. There is a growing interest in the bacterial composition of the gut microbiome of humans (structure) and the role of the microbiome in human diseases (function). Many methods are used to define the structure and the function of a microbial community and there are concerns about how the use of these varying methods can impact the reproducibility of microbiome research. In this dissertation, we aimed to determine how different measurement techniques impacts the understanding of the structure and function of the gut bacterial communities in humans and in model systems such as non-human primates and rodents. Along with determining these different techniques to quantify the structure and function of the gut microbiome, this dissertation applies these different techniques to determine how dietary sugars impact microbial community composition and determine factors that are associated with the gut microbiome in patients with colorectal adenomas, a benign tumor which is often times a precursor to colorectal cancer.