The microbiome is the organisms and their gene content that occupies a particular space, perhaps most saliently the gut microbiome which has diverse and important implications in organism functioning. The previous decade has had a veritable explosion of microbiome literature owing to the development of 16S gene sequencing, which can taxonomically identify the microbes in a microbiome, and refinement of analytical and bioinformatic techniques for more effectively extracting information from this data. Despite this, the chemistry of the microbiome, a key facet in health and medicine, remains under-explored. We present here three case studies which utilize 16S sequencing and subsequent analysis to explore the microbiome through a chemical lens, making strides in understanding the physiology of diverse subjects of neointimal hyperplasia, Alzheimer's disease, and gamma-aminobutyric acid supplementation. This is followed by a review of microbiome precision medicine to contextualize these findings and point towards future research in the field.