Statistical evaluation of diet-microbe associations

Statistical evaluation of the association between microbial abundance and dietary variables can be done in various ways. Currently, there is no consensus on which methods are to be preferred in which circumstances. Application of particular methods seems to be based on the tradition of a particular research group, availability of experience with particular software, or depending on the outcomes of the analysis.

We applied four popular methods including edgeR, limma, metagenomeSeq and shotgunFunctionalizeR, to evaluate the association between dietary variables and abundance of microbes. We found large difference in results between the methods. Our simulation studies revealed that no single method was optimal.

We advise researchers to run multiple analyses and focus on the significant findings identified by multiple methods in order to achieve a better control of false discovery rate, although the false discovery rate can still be substantial.