Comparative Analysis of Core Microbiome Assignments: Implications for Ecological Synthesis
Gordon Custer, Maya Gans, Linda T. A. van Diepen, Francisco Dini‐Andreote, C. Alex Buerkle
Abstract
Different methods are commonly used to assign core microbiome membership, leading to methodological inconsistencies across studies. In this study, we review a set of the most commonly used core microbiome assignment methods and compare their core assignments using both simulated and empirical data. We report inconsistent classifications from commonly applied core microbiome assignment methods. Furthermore, we demonstrate the implication that variable core assignments may have on downstream ecological interpretations. Although we still lack a standardized approach to core taxa assignments, our study provides a direction to properly test core assignment methods and offers advances in model parameterization and method choice across distinct data types.