Many clinically relevant microorganisms associated with health and disease are present at some level in the gut of healthy individuals. The clinical significance of microbiome test results is determined not only by the identity, but also the quantity of distinct species and genera within the context of a healthy reference range. To determine the healthy reference range for the 28 targets, we established a cohort of 897 samples from self-reported healthy individuals from the uBiome microbiome research study (manuscript in preparation). Microbiome data from this cohort were analyzed to determine the empirical reference ranges for the 14 species and 14 genera. For each of the 897 samples, we determined the relative abundance of each target within the microbial population. This analysis gave rise to a distribution of relative abundance for each target in the cohort (Fig 3, S3 Table). These data were used to define a central 99% healthy range with confidence intervals for each target. Many of the targets show significant spread, emphasizing the importance of microbiome identification in the context of a reference range. For example, the pathogen C. difficile is found in ~2% of the healthy cohort, and thus we define a healthy range for it from 0% to 0.18% relative abundance. Although C. difficile is an opportunistic pathogen that can cause severe diarrhea, especially among antibiotic-treated hospitalized patients , our results confirm that asymptomatic C. difficile colonization is not uncommon in healthy individuals . Although all taxa were present in at least one of the healthy individuals, the upper limit of the reference range of the relative abundance was found to be quite high for some taxa (e.g., 63% for Prevotella and 49% for Bifidobacterium). Two species are not represented at all within the central 99% of the healthy cohort: Vibrio cholerae and Ruminococcus albus. The absence of V. cholerae is suggestive of its pathogenic nature and its relatively rare occurrence in the developed world. However, R. albus, has previously been found to be enriched in healthy subjects in comparison to patients with Crohn’s disease .