Hi @quinnr, the way to think about this figuring out how to partition variation in the metabolites with respect the microbes. If you look at co-occurrence plots, it is difficult to see which microbes have the strongest relationship with regards to the metabolite abundances. Biplots can help you cut through the noise and see the top microbial drivers of metabolite variation.
The cystic fibrosis example is the one that I like to use to showcase this. From the biplot, you can see there are really only two groups of microbes, which turn out to be largely characterized by anaerobes and pathogens. The longer the arrows are, the more variation those microbe explain.
There is another extensive discussion on how to interpret biplots that maybe worth checking out