Just a quick post here. I have been reading this paper: Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data by Jeroen Raes et al. in Molecular Systems Biology. This integration they try to pull off in the paper is to me where we need to move as a field (i.e., microbial ecology) in order to make full use of metagenomic data. The paper provides a nice overview of microbial biogeography too. Definitely worth a read.