I have an experiment where I’ve compared the gut and stomach microbiomes of a territorial reef fish receiving enriched nutrients to those without. I found that both stomach and gut microbiomes increase in diversity when nutrients is added but interestingly enough DeSeq and ANCOM and PICRUST all highlight taxa that are at higher relative abundances in the controls.
So from what I can tell, the increase in diversity in the enriched samples is due to an influx of rare taxa that do not have high enough abundance to statistically mean anything. The other possibility is that adding nutrients increases the rate of unassigned taxa which would also explain the results. How might one move forward to better explain the increase in diversity?
I realize I am omitting a lot of important information so feel free to ask for more info if needed.