SRP286727 PRJNA667969 A metabarcoding guideline for profiling amoeba communities Amoebae has drawn increasing attention due to their crucial ecological roles and potential health risks in natural and human-made environments. Currently, 18S rRNA gene sequencing is the most popular method to analyze the amoeba community and their diversity along with morphological approaches. However, until now, it is not clear what is the best primer pair for 18S rRNA gene amplification in the amoeba community analysis. In this study, we compared the four most common primer pairs in revealing the community diversity, composition, core species, and assembly process of amoeba communities from water and sediment environments.