Hi!
I am a new user of quiime2 and would like to know if anyone knows if it is possible to run any type of analysis to understand what the taxonomic drivers are for differences between sample types (beta diversity)?
/Susanne
Welcome @SusiDus!
See ANCOM for a method to test differential abundance between sample types.
Good luck!
Looks very promising. Thank you!
/Susanne
Hi!
We are trying to identify microbial drivers (signature microbes) for three different subsystems in an underground Mn deposit. For this we have conducted a differential abundance analysis using balances in gneiss (“ANCOM assumes that few (less than about 25%) of the features are changing between groups" and we see from the analyses that we are above this level). When doing pairwise comparisons in gneiss one can choose at what level you want the analysis done (ex. level 3 corresponds to order and level 4 to family). The analysis then produce proportion plots based on log ratios between different groups of taxa. I do however not understand why I in some plots (not all) get more than one line (bar) for the same order (see attached document which is a proportion plot at level 3, i.e. order level). Is not the whole idea of choosing taxonomic level to group all OTUs that belong to this taxa at this specific level together. In the example I get 3 different lines for mycococcales.
Grateful for help,
Susanne
I believe those are individual ASVs that all share the same taxonomic label. This is not grouping the ASVs by taxonomy, rather it is just showing the top N features that are associated with each group, and labeling them by taxonomy rather than the feature ID.