Best Differential Abundance Tool for Microbiome Studies and Ensuring Cross-Study Comparability

Question

[benkosta]

Hi everyone,

I’m currently working on a microbiome study and need advice on selecting the most appropriate tool for differential abundance analysis. I came across the study by Nearing et al., which highlighted that different tools (e.g., LEfSe, DESeq2, ANCOM-BC2, etc.) can identify drastically different numbers and sets of significant ASVs, and that the results are influenced by data pre-processing methods.

Given these challenges:

Which differential abundance tool would you recommend for robust and reliable results? How can the results of my study be made comparable with those of other studies, considering the variability introduced by different tools and pre-processing methods? Any insights, recommendations, or shared experiences would be greatly appreciated!

Thank you in advance!

[benkosta]

Any ideas or help on this matter?