OK I have been dreaming about doing something like this for many years. One of the potentially most useful aspects of shotgun metagenomic data is that you get a sample of many/all members of a microbial community at once. And then in theory one could look across different species and taxa and ask – do they all have similar adaptations in response to some sort of environmental pressure. There have been a few papers on this over the last few years (e.g. check out this one from Muegge et al on Diet Driving Convergence in Gut Microbes). But this new paper is really the type of thing I have been hoping to see: Environmental shaping of codon usage and functional adaptation across microbial communities. Basically they looked at codon usage in organisms in different metagenomic samples and found major metagenome specific signatures, suggesting that different taxa were in essence converging on common codon usage.
The paper is definitely worth a look.