Diversity measures provide information about the composition of a microbial community. Diversity analysis, in the context of the intestinal microbiome, is classified into alpha diversity and beta diversity. Innovation in bacterial DNA sequencing methods has allowed researchers to describe the intestinal microbial community with unparalleled ease and precision. In 16S rRNA sequencing, characterization of the microbial community using the sequence data begins by either clustering the 16S reads or comparing individual reads to a reference database. Marker genes, specific genes that are well characterized and sequenced across multiple bacterial strains and species, are mapped to a reference database to identify microbes. 16S rRNA sequencing is a relatively simple technique with many advantages over more complex sequencing strategies, including its low cost, standardized protocols—including sample preparation, sequencing, and downstream analysis—and high-quality reference databases against which to map obtained sequence data.