Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing.

Differential abundance tests yielded varied concordances, and amounts of detected DA signatures. Some methods were more concordant than others on both filtered and unfiltered data, therefore, if consistency with other study methodology is a key goal, one might choose among these methods. Even still, using one method on one dataset may find true associations, but may also detect false positives. To help lower false positives, one might analyze data with two or more DA methods to gauge concordance, and use a built-in replication dataset. This study will hopefully serve to complement previously reported DA method comparison studies by implementing and coalescing a large number of both previously and yet to be compared methods on two real gut microbiome datasets.