Merging two different runs resulted in very different microbial popultion

[jwdebelius (Justine Debelius)]

Hi @ronnie,

Welcome to the QIIME 2 forum!

This is a semi common problem, particularly for low biomass samples, with this study being kind of the worst case senario.

There are some option for handling this, which are discussed in this thread, but ultimately, it's a challenging problem.

Discussion: methods for removing contaminants and cross-talk

Just to add further to this discussion, I've previously used decontam prior to it being incorporated into QIIME 2, and whilst I'm a huge fan of the principles it's built around, it didn't work fantastically for my samples. I will caveat that as I did only attempt the prevalence method with 2 negative controls (one kit negative and one sequencing negative) for around 20 samples, which is likely too low a number of controls to have any real statistical power, I'm not sure what the ideal number of …

Best,
Justine