I need some help in describing to a non-expert why it is generally not a good idea to infer the metabolic ability of an environment based on the metagenomic assembly, and instead it is better to use the retrieved MAGs. This person sees all of the available genes in the assemblies and concludes that the two environments are not very different from each other. Meanwhile, the retrieved bacterial MAGs show that the two environments are indeed different and have a different metabolic repertoire. I tell them that the MAGs are the representation of the organisms that are most likely to be present and alive in the environment, as their metagenomic read coverage is high enough to assemble MAGs. That seems to go over this person's head and they respond that we dont have metatranscriptomes so we cant talk about who is alive/active. I agree, but the MAGs give the best option of the organismal DNA present since there are lots of envrionmental DNA that get transported into an environment but doesnt make up the endemic bacterial community.
Anyone have recources to prove to this person that my MAG focused analysis is the correct way to assess metabolic potential in an environment?
