Microbiome differential abundance methods produce different results across 38 datasets

Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale studies systematically exploring the appropriateness of using these tools interchangeably, and the scale and significance of the differences between them. Here, we compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups. We test for differences in amplicon sequence variants and operational taxonomic units (ASVs) between these groups. Our findings confirm that these tools identified drastically different numbers and sets of significant ASVs, and that…

• CR
  Canada Research Chairs
• RN
  Research Nova Scotia
• NS
  Natural Sciences and Engineering Research Council of Canada