As above, I am wondering if there are any public multi-omics data sets online and available to download? The sort of data might be transcriptome, proteome and metabolome all gathered from the same samples.
Jill Banfield's group does this quite a bit. I know that there is metagenomic and metaproteomic data from the Acid mine drainage communities. They have also done work more recently with acetate amended aquifers which has both genomes and proteomes.