The communities of microorganisms living within and on us collectively constitute our microbiome. The microbiome has been linked to numerous health problems, such as autoimmune diseases, diabetes, cancer, and psychological disorders. We describe the challenges that accompany developing quantitative measurements for the microbiome. Hurdles in this process often begin with patient obliviousness and unwillingness to donate fecal samples. Even with cooperative patients, efficient methods of sample collection that maintain viable microorganisms for analysis have proven difficult. Minor faults in sample collection can lead to incorrect microbiome characterization, especially when trying to determine the function or disease likelihood associated with a sample. Finally, even if the process of analyzing a sample is successful, what do the analyses of microbiome samples mean to the individual or a health care practitioner? How can we decide what is considered a normal microbiome state with such large variation among individuals?