Sample Preparation

We unfortunately didn't have a proper "uninoculated control" throughout the whole thing because we did this over 3 rounds of experimenting with slightly different reagents (different lots and vendors of DME for example). It would have been expensive to sequence a dozen DME samples. That said, we did verify prior to the experiment that we wouldn't pick up an overwhelming amount of barley DNA in the study, so we know we're not just getting swamped out with malt DNA. Plant sequences did show up in our eukaryotic microbiomics, but that was unavoidable. I'm sort of amazed we didn't see a big signal for chloroplast and/or mitochondrial DNA in the bacterial analysis.

Also, since the sequencing doesn't discriminate between dead cells and living cells, a type of control we put in to place was before anything was inoculated, we plated a portion of the nutrient-rich buffered starter (basically just LME, CaCO3, and yeast nutrient) after autoclaving to ensure nothing grew. All the samples came back negative (no growth). And yes, that would be good to note in our results :)