Collections of probability distributions arise in a variety of statistical applications ranging from user activity pattern analysis to brain connectomics. In practice these distributions are represented by histograms over diverse domain types including finite intervals, circles, cylinders, spheres, other manifolds, and graphs. This paper introduces an approach for detecting differences between two collections of histograms over such general domains. To this end, we introduce the intrinsic slicing construction that yields a novel class of Wasserstein distances on manifolds and graphs. These distances are Hilbert embeddable, which allows us to reduce the histogram collection comparison problem to the comparison of means in a high-dimensional Euclidean space. We develop a hypothesis testing procedure based on conducting t-tests on each dimension of this embedding, then combining the resulting p-values using recently proposed p-value combination techniques. Our numerical experiments in a variety of data settings show that the resulting tests are powerful and the p-values are well-calibrated. Example applications to user activity patterns, spatial data, and brain connectomics are provided.