Differential abundance outputs.

Hi, folks!

I am trying to identify features that are differentially abundant across three groups (dis, prb and ctr) First, I applied ANCOM to determine which genera are differentially abundant I got W equal to 0. Then I try using qiime diversity adonis and I got R squared = 0.03. Which is the same results with ANCOM. But when I have run Gneiss I can't see that I have the same idea. I know that the proportion plots are there to help understand the distribution of the species in each part of the balance.

I was wondering if this result was telling me that there was a difference in abundance of Streptococcus between my groups–is this accurate?
If this is true, why ANCOM failed to detect significant abundances among the groups? I expect at least Streptococcus suis to be different as I first collapsed the data at level 6. In order to determine if I have different Streptococcus species among my groups, I combined the dis and prb into one group but still can not report the results!
I have attached the both files for each test and adonis output as well.
Here is my code for ANCOM:

qiime composition ancom --i-table com-collapsed-l6.qza --m-metadata-file geniss.tsv --m-metadata-column diagnosis --o-visualization sick-ancom-subject.qzv

sick-ancom-subject.qzv (427.0 KB)
l6-ancom-group.qzv (427.7 KB)
group-balance-taxa.qzv (450.9 KB)
sick-balance-taxa.qzv (470.9 KB)
adonis-group-significance.qz.qzv (288.2 KB)

@mortonjt any comments are valuable.

I really appreciate any input!

Best,
Maysa

A couple of clarifying points, first that balance looks like it is Streptococcus vs Moraxella, so there are two hypotheses, either Streptococcus changed or Moraxella changed. Its not possible to infer which one has actually changed without additional assumptions.

Regarding why ANCOM disagrees, it’s likely because of the differing assumptions. In order to infer which species has changed, ANCOM assumes that a certain percentage of microbes aren’t changed in abundance. The assumptions behind Gneiss are based on the choice of tree to perform the analysis.

I also want to recommend checking out other differential abundance tools such as aldex2 and songbird, and in addition to the other posts related to differential abundance.

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