The hypothesis of a 'core' community receives poor support when confronted with simulated and empirical data

The field of community ecology is evolving rapidly as researchers are able to tie functions of systems to variation in taxa. In inferring processes, functions, and causal taxa, common practice is to assume a ‘core’ community can be defined. The core refers to a group of taxa found across samples, and statistically, is the discretization or categorization of continuous data. Assuming thresholds in abundance exist, and that a core microbiome exists, has the potential to be misleading. Rather, the existence of a core set of taxa should be treated as a hypothesis with support from empirical observations. An additional challenge is that there is no standard set of criteria for core membership. Consequently, comparison across studies is often impossible. We considered four common methods for defining a core and applied them to 25 simulations that cover a range of plausible communities and two published microbial data sets. Next, we used hierarchical clustering and bivariate plots of mean taxon abundance and variance to evaluate each method. Assignment of taxa to the core varied substantially among methods. Across simulations and published data sets, hierarchical clustering of taxa based on their abundance and prevalence (variation) offered no support for a core set of taxa. The categorization of taxa into sets corresponding to a core community and other taxa has the potential to be misleading. Given that the concept of core communities received poor support from data, the concept is questionable and should not be used without testing its validity in any particular context.