Hi @xchromosome,
You are correct to have concerns about this. This isn't the first time we've seen ANCOM identify features significantly different with very low W values. See this post for more details. However, I should also mention that ANCOM is much more powerful for larger datasets, meaning if you were to compare your data at the Genus level instead of the Phyla you would have much more meaning results. You are only comparing 7 Phyla which means the max W value you can get is 6, which doesn't allow for alot of certainty. This may be why you are seeing differences that may not actually be true.
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