skreling
commented
3 years ago The bat and wolf datasets were both from fecal samples and the mouse was gut microbiome!
Quantification of metabarcoding diet is somewhat controversial, but there are 2 main methods - relative read abundance and frequency of occurrence. I think for most applications of metabarcoding RRA is generally utilized as a metric for relative abundance, but diet is a little behind and still using FOO pretty frequently, but both methods have pros and cons and generally are relatively untested in terms of accuracy (esp for diet). As an aside most of the dereplications tools I've used have also kept track of the number of reads of each sequence type which has been really helpful!
Wow, this is all really cool stuff! I have basically zero familiarity with metabarcoding, so I just had some questions about it!
First, what's the original source of your samples from the bats/mice/wolves? Are these fecal samples, gut samples, something else?
I was also wondering about the tools you're using! It looks like both Obitools and DADA2 have a step that involves dereplication. Does this mean that your results are just looking at presence/absence, or are there methods to quantify abundance?
Anyway this is all really neat and now I'm gonna spend a while checking out Obitools and DADA2!