I know a few studies (like Western English Channel) where analysis of biodiversity was conducted over time. However, all of the studies I found were based on the sequencing of 16S rRNA amplicons. Do you know any research where full shotgun sequencing was done in time-course on the same sample/spot?
There's a few places with time-course data for WGS metagenomes, but for me the unequivocal choice would be MG-RAST. I was not impressed with early versions - so I ignored the site for a while - but in the last year it has really ramped up and now there are 64,000 metagenomics datasets available, and plenty open WGS data sets to choose from.