After running alpha and beta diversity metric, I have stablished I have significant differences between my two groups (A and B) for quantitative (Bray and Weighted) but not qualitative (Unweighted/Jaccard) or presence-absence (alpha, Shannon etc...).
Now, I would like to establish a microbiome core between these two groups and establish the abundance significance at different levels.
Is there an option/feature in QIIME to determine differential core-significance between two sample groups (Subject) on various taxonomic levels? And access those taxons that differ?
My desired output ( I could build it up myself, but aiming to get the following data).
Tax Level; Number of differentially abundant taxons; Significance;
A; B; p-value ;
Phylum ;2 ;4 ;0.005
Class ;x ;x; 0.02;
Order; x; x; x;
Pfamily; x; x; x;
…
@ecg, it sounds like you’re looking for a QIIME 2 pipeline or visualizer capable of collapsing tables to various taxonomic levels and running differential abundance methods on them?
If I’m on the right track, I don’t think that tool exists yet. You might want to consider building it as a QIIME 2 plugin and publishing it to the library, if you think other users might benefit. We’re always happy to support development questions in the developer discussion category of this forum.
As a side note, the core-features action might be useful for you. It selects core features based on the fraction of samples in which those features appear, so depending on the questions you’re trying to answer, you may have to group your table into sample groups before running.
Thanks @ChrisKeefe Chris, yes, I have done it already like this, but it does not tell you significance, only number of features per taxonomic level and fraction of features.
ie: It would be interesting to see (from a functional perspective), two groups share high amount of taxons at phylum level (ie. proteobacteria) but it is under lower levels where these groups are different (as expected). I would like to know at what point that is significant.
Yeah, I had a feeling that would be the case. Sorry I didn't have a more exciting answer for you! Do let us know if you decide to build this up into a plugin or similar. Always happy to answer questions about that kind of thing here!
Do let us know if you decide to build this up into a plugin or similar. Always happy to answer questions about that kind of thing here!