One of the arguments made in In Defense of Food is that the nutritional quality of food varies with where and how it is raised or grown. Wild game may have a different nutritional profile than farm raised varieties. One of the possible reasons that people living near the arctic circle who eat very little vegetable matter but subsist off of reindeer meat are healthy is the differences in type and amount of fat in the meat. Differences in diet between factory farm beef raised on grains and grass fed beef create differences in nutritional profile.

Recent news bolsters this argument. Tilapia, a fish, has become popular in recent years. A study shows that factory farm raised tilapia have low levels of healthy omega-3 fatty acids and high levels of unhealthy omega-6 fatty acids. Higher levels of omega-6 than bacon. It should not be surprising to learn this, given that modern agriculture is based on the idea of feeding plants or animals according to “inputs” and not the kind of food they would eat in nature. It also shows that we are what our food animals eat (as Omnivore’s Dilemma explores).
US News has a good article on the problems of factory farm-raised fish, such as tilapia and catfish Popular Tilapia Might Not Help Heart