Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves data processing, statistical analysis and graphical display. Such an analysis requires expertise for installation, data processing, programming skills and computing infrastructures. Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available (see benchmarking – Table 1). SHAMAN is specifically designed for non-expert users.