This is a cool arrangement, except for maybe two things. First it’s a bit of a raw deal for some of the individual microorganisms that, in spite of their service to the cow, get digested themselves. I think I mentioned that ruminants can derive more than 100 g of protein per day from digestion of their endosymbiotic microorganisms.
The other problem, from the more global perspective, is the amount of burping, etc. that cows do because of this association. About 17 percent of the methane in the atmosphere comes from cows and other ruminants as they digest food. This greenhouse gas is formed as their stomach microbes metabolize carbon dioxide into methane, which is “vented” to the atmosphere.
There is research underway to try to reduce the amount of methane Bessie produces, including making “burpless grass” and trying to introduce less burpy microbes into cow guts (from kangaroos, which have more microbes with better manners).
You can read about the efforts to create “burpless” grass in this article from Sciencedaily.com
And listen to an NPR interview about the Australian researcher working on transfer of microbes from roos to cows.
It’s a bit older, but there is a nice NPR story on greenhouse gas production from sources (like cows) other than big industry. This was aired on Ira Flatow’s show, “Science Friday”. I recommend tuning into the show when you can; it airs on, well, Fridays - locally on KCLU (102.3) from 1-2pm. It’s also online at http://www.sciencefriday.com/