Hi Ruby,
Okay, I just wanted to check. Sometimes, the taxonomic comparison can be really similar at, say, phylum level, but you can see more when you go deeper.
Would you mind running qiime diversity beta-diversity on your samples with the bray-curtis and jaccard distance and letting me know the distance between the two samples. You'll need to rarify the table, first.
That's good. So, it's less likely that there was an error at the import. The training sounds fine to me. The resason Im asking is because Im concerned there was a mix up somewhere and the same sample got run twice with different names.
I would suggest going back and double checking your lab notebook, as well as the Illumina sample sheet, if you have access to that. These questions are to make sure you didn't run the same sample twice, somehow. And, if you did, to figure out where so you can limit what you have to re-do.
My last concern with these samples is that if they're (Im guessing) biopsy samples from the lung and kidney, they're probably very low biomass. I would absloutely check your negative controls, to see what (if anything)_shows up there. There's also discussion of a positive single culture control, so if you have something like that, worthing checking what shows up there. Reagent contamination is a fun and interesting problem in this field, and there have been a lot of discussions on this forum. There's a big thread here, which is where I think I might start. I dont do a ton of work in low biomass samples, but Im always interested, so if you do a lit review and/or find a good paper, please share it!
Best,
Justine