Although they’re microscopically small, microbes have critical effects on the world around them. The development of new technologies such as next-generation sequencing (NGS) has enabled scientists to examine what shapes microbial communities in the wild. A novel concept, Phylogenetic Core Groups (PCGs), aims to search for a taxonomic classification revealing the selective forces imposed by the environment, hence, complementing traditional classification methods. But because microbial communities are sensitive to environmental fluctuations and we observe only a small fraction of these communities, it is difficult to disentangle these selective forces from community composition only. A new study proposes an improved conceptual framework to refine the determination of PCGs. Starting with a regional pool of microbial species, scientists can observe changes in the community composition and relate these changes to environmental variables. Determining the relative contribution of stochastic vs. selective processes the microbes’ environments can be classified into different niches. Although this framework requires solving several sub-problems for each dataset, it presents a consistent method for evaluating genetic, stochastic, and environmental processes, coherently unraveling the complex factors affecting microbial communities.