Hello everyone,
I’m working with microbiome data using ANCOMBC2 and encountered an interesting discrepancy between taxonomic levels that I’d like to understand better. Specifically, my genus-level analysis with ANCOMBC2 reveals that certain Bacteroides genera are significantly more abundant in the control group, as indicated by a statistically significant log2 fold change. However, when I analyze the data at the phylum level, this difference is no longer detected in Bacteroidota phyla.
Has anyone else come across this kind of discrepancy, and if so, how do you interpret it? Could the genus-level differences be driving effects that aren’t observable at the phylum level? Additionally, are there recommended approaches or alternative methods that might help confirm or further explore genus-level findings?
Any insights or advice on how to approach and interpret these results would be greatly appreciated. Thanks in advance for your help!
Such discrepancies are perfectly normal. Aggregation of count data at phylum or genus level generates different count data and so different results.
If you decide to go for a differential abundance analysis at the genus level, check that the genera that significantly change across your condition are amongst the most abundant ones.