The direct possibilities for influencing food safety and public health by farm animal breeding and reproduction are limited.
Improving food safety will be possible by breeding in an indirect way, in decreasing the incidence of food-borne infections.

Breeding organisations attempt to improve the animals' natural genetic resistance to disease, which reduces the need for medication and the occurrence of zoonoses and improves food safety and human health.

For some of the responsible zoonotic organisms, such as Salmonella and Campylobacter, there is genetic variation in the susceptibility of farmed species to carrying or shedding these organisms. If we understand better the cause of this genetic variation, we can determine the sustainable breeding strategies to exploit such variation. New zoonotic infections will emerge and the importance of as yet poorly characterised zoonoses will become apparent.

At a wider level, farmed poultry and pigs play a role in the evolution of pathogenesis of human infections, most notably influenza. There are opportunities through genetics/genomics research to reduce the risk of the evolution of increased pathogenesis of human influenza, via recombination with non-human influenza viruses. Such opportunities might include GM chickens resistant to avian influenza.