People who know me know that I often bitch about industrialised food production. Particularly indistrialised animal farming. The recent E-Coli caused food poisoning scare in the US (3 dead, 200 hospitalised) has been traced back to industrial cattle farming.
In an article for the New York Times, Michael Pollan describes how the e-coli got there. Basically it's a strain of the bateria that originated in feedlot cattle that are fed on grain (and whatever else). It does not appear in grass fed cattle.
Besides being a breeding ground for new super-bugs (the overuse of agricultural anti-biotics has well known consequences) there is another problem, as explained by Pollan. By industrialising both animal and vegetable faming we have seperated the old plant->animal->manure->plant cycle and produced to seperate problems. The plants don't have fertiliser, and the animals produce ~1 billion tons of manure every year. The fertiliser problem has been "solved" by using artificial nutrients, but the manure problem has no solution.
Tie this in with the problems of massively centralised food production (an outbreak in a single food supplier caused a nationwide food poisoning event) and we see yet another downside of industrial food production.