Yes, that makes sense. Because you have unique primers, the nb-skl classifier would work best after customization. You could also try a top-hit LCA classifier like vsearch or blast, which may benefit from customization but does not require it.
We should have mentioned this earlier, but there's a new plugin for building custom databases.
This sounds great! You can still detect specific microbes that server as biomarkers for this change then give them taxonomy labels later. And measuring the magnitude and significance of microbiome variation does not use taxonomy at all.
