Microbiome differential abundance methods produce different results across 38 datasets

🤖 Plain-English Summary

Identifying differentially abundant microbes is a common goal of microbiome studies. ALDEx2 and ANCOM-II produce the most consistent results across studies and agree best with the intersect of results from different approaches.

🔑 Key Findings

• 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.

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