One of the things that has gotton me very interested in the examination of domesticated animals, is their ultimate effects down the line on other aspects of human health. As I discussed earlier, the reckless feeding of antibiotics to farm animals may have effects down the line on propagating antibiotic resistance to potential human pathogens. There are other effects on human health that are important as well, which of course primarily stem from our animal husbandry techniques.
Chickens for one, are commonly implicated in food poisoning by the organism Salmonella enterica. Salmonella is a relatively clever pathogen, being capable of escaping from the chickens gut and then invading the tissues of the bird. In addition to this, the organism is even smart enough to get into the developing eggs of the chicken meaning nothing about the animal is salmonella free. Unfortunately, it turns out that part of the reason why this is so common is because the chickens are kept so closely together. The young chicks have no inherent microbiota and the salmonella which gets into the chicks gut, from food mixed with feces or particles picked up from general pecking. This basically enables the salmonella a free opposition-less ride all over, increasing the amount of salmonella in all the chickens.
Another example is the diet of cows and a more recent human pathogen, Escherichia coli O7:H157. Cattle in some places in the world are fed on a carbohydrate rich diet, which when metabolised by the commensal bacteria in their rumen (cattle, unlike us, have a five chambered stomach) causes a considerable drop in pH. E. coli O7:H157 is more acid resistant than the normal bacteria that live in the rumen, meaning that as the pH of the rumen drops it also provides an advantage to the E. coli because it no longer faces the same competition. This means that you have the pathogen proliferating from its normal low numbers to much higher numbers in the gut.
The point that is important here is the addage "you are what you eat" is certainly very true. In our case, when we use practices that select and aid the proliferation of pathogens in the animals we eat; it's little wonder that we end up eating those pathogens more often as well.