Thank you so much for pointing me toward the well-to-well contamination paper and the contamination filtering on the forum. I will definitely check them out. I will also check on the PCoA step as you suggested.
For now, can I ask you a naive question? How do I know if my samples are low biomass or high biomass samples? They are human stool samples so I am guessing they are high biomass?
Your stool samples are definitely high biomass. As far as knowing the sample type, umm… I think most people learned empirically or just sort of guess. I tend to think of stool, oral, and most soil as high biomass. Skin might be medium biomass. Low biomass will be things where it’s hard to get bacterial DNA, usually because there isn’t a lot of DNA to be had. Those might be things like built environments, mummy teeth, infants in the PICU, or space ships.