Differential abundance analysis in ALDEX2 (or similar) at a higher taxonomic level


I have been trying to do some differential abundance analysis on my data using the ALDEX2 plug in, and despite the fact there is clearly a big difference between my groups in terms of relative abundance in stacked bar plots, on ALDEX almost nothing is coming up. I have a feeling this is because it is analysed at the OTU level, however in my plots even at a species and genera level there are clearly big differences.

e.g in my control bacteroides genera is ~10% rel abundance
in my treatment group this genera is almost 50% rel abundance

  in my control bacteroides acidfaciens species is <5% rel abundance
  in my treatment group this species is almost 40% rel abundance

This is true for a number of other genera and species that look really different. Yet when I run aldex it says just one OTU is significantly different (see attached plots, as a side note the axis on the effect vs q plots are a bit weird using qiime view and I can't really see the significant points). And to be honest im still a little confused about what the threshold for significance is.

I am wondering whether I am using the tool correctly, or if there is another tool that I could use instead to quantify / statistically analyse the changes that I can clearly see in my stacked bar plots.

Would appreciate some guidance on this.

Thank you