Ever wonder what goes on in a cow’s multi-chambered stomach? Probably not. I did think about it a little more after a trip to a teaching farm during grad school where we saw a cow with a fistula. This hole provides access to the cows stomach so that samples can be drawn of the community living in the gut and understand how the bovine stomach can digest the recalcitrant cellulose of grasses.
Of course all kinds of lovely things live in the dark, anaerobic environment. In fact there is a delicately balanced community of species. When cows are fed corn instead of grass this affects the rumen acid content and allows pathogenic E. coli like O:157 to survive. So far I don’t seen any JGI proposal for sequencing of the gut communities of rumens, but maybe that should be proposed.
Rumen fungi are probably not on your keyword list, but these fungi are extremomophiles living in highly anaerobic environment. A paper in Microbiology details an analysis of the genome of the anaerobic fungus Orpinomyces.