Comparisons of microbiome communities often use pairwise distance measures (beta-diversity). Current analyses require the primary data if another investigator wants to add or compare independent data. We propose standard reference measurements to simplify microbiome beta-diversity analyses and facilitate independent validation and comparisons. Using stool and nasal reference sets from the Human Microbiome Project (HMP), we computed mean Bray-Curtis distances to each reference set for each new sample. Each new sample thus has two mean distances that can be plotted and analyzed with classical statistical methods. We studied independent (not reference) HMP subjects. Hotelling tests demonstrated statistically significant differences in mean distance vectors between all pairs of body sites (stool, skin, nasal, saliva and vagina) at the phylum, class, order, family, and genus levels. The use of reference vectors simplifies analyses of beta-diversity and facilitates the independent validation because others can compute distances to the same reference sets. Standard statistical methods for survival analysis and logistic regression apply to mean distances to reference sets.