The human microbiome plays a fundamental role in human health. These microbes, that live on and inside of us, perform a range of critical functions, including vitamin synthesis and the production of short chain fatty acids. Research over the past decade has highlighted relationships between the microbiome and diseases like Inflammatory Bowel Disease, Nonalcoholic Fatty Liver Disease, Parkinson’s, cancer and more. Concurrently, research has shown a remarkable degree of variability in the microbiome among individuals, with substantially more variation than peoples genomes. The factors related to the dynamic ranges of microbes observed are not well understood, nor is it known whether certain configurations are healthier or may predispose you to disease. Two major limitations are data: a small portion of the human population has been sampled, and the collective set of microbiome studies performed have incompatible standards. Within the American Gut Project, and its global extension The Microsetta Initiative, we are combating these limitations through infrastructure that allows virtually anyone to participate. To date, over 20,000 have submitted microbiome samples. The data produced, including a detailed voluntary questionnaire, are released de-identified into the public domain for anyone to reuse. In this talk, we discuss the importance of citizen science for the microbiome, and some of the challenges encountered since project inception in the fall of 2012.