Unraveling Key Features of Microbial Alpha-Diversity Metrics and Their Practical Applications

Abstract Studies of microbial communities vary widely in terms of analysis methods. In this exponentially growing field, the wide variety of diversity measures and lack of consistency make it harder to compare different studies. Most existing alpha-diversity metrics are inherited from other disciplines and their assumptions are not always directly meaningful or true for microbiome data. Many existing microbiome studies apply one or some alpha diversity metrics with no fundamentals but also an unclear results interpretation. This work focuses on a theoretical, empirical, and comparative analysis of 19 frequently and less-frequently used microbial alpha-diversity metrics grouped into 4 proposed categories, including key features of every analyzed metric with their mathematical assumptions, in order to provide a deeper understanding of the existing metrics and a practical implementation guide for future studies.