Reflection on Metabarcoding
Metabarcoding is probably the first thing that comes to mind for me when I think of eDNA. Partially because my own work centers around metabarcoding of gut contents of lobster larvae, but also because I have a focus on ecology where metabarcoding techniques have shown promise in helping us measure species richness (if not abundance). I think I am lucky to be dipping my toes into the field of eDNA right now when many universal priming/metabarcoding regions have already been identified, but something that this week’s paper highlighted is that these regions still need careful evaluation. For a true analysis of an area’s species richness, multiple regions should clearly be targeted, either through multiplexing or running samples through the pipeline multiple times. One thing I wonder is has there ever been a robust test of how primer design affects metabarcoding results? Shane brought up the question of “How many degenerate bases is too many?” I believe that could actually be quantified through a really carefully designed study where multiple primers hitting the same region and of the same length but with different amounts of degenerate bases were tested against a very carefully assembled mock community. We could then actually quantify how many reads we get and how many unique taxa are identifed as you increase the number of degenerate bases. Likely you could repeat this study, but vary primer length instead. The question then is how applicable is that data to other studies/taxa/metabarcoding regions? I doubt anyone really has a good idea how to answer those questions right now, but I feel like these are the types of questions we may want to think about when it comes to establishing eDNA, and metabarcoding in particular, as common tools of the modern scientist.