Kent Sepkowitz is a doctor I like. He's actually willing to admit more people have been saved from disease by ditchdiggers than by doctors.. What he's worried about is deaths from bacterial contamination of food, and I agree that trying to make the food supply utterly safe is impractical. Well, at least impractical for most people. The "pick two" for food seems to be "cheap, safe, tasty" and there's not many people willing to subsist totally on MREs or blow half their income on food. So Sepkowitz advocates dosing people with just enough pathogens to train their immune systems to deal with the inevitable contamination they'll have to deal with.
Rather than frantically throwing money at new ways to eradicate the pathogens that reside in shit, we should fund the boring scientists who focus on untangling the intricacies of the gut's immune system. Labs, answer this: How much shit can we safely eat and, as importantly, how much must we eat to remain healthy?
What I love about this is that a doctor is looking at the vaccination question from the other side, trying to establish minimum and maximum total amounts for the immune system insults. It's a wonderful change from the folks who insist that vaccines are good, therefore more vaccines are better. A good next step would be performing their studies on statistically valid sample sizes. After that they can analyze the distribution of the reactions to see what fraction of the population would handle this badly and how to recognize them, instead of calculating a mean optimum dose and prescribing it for everyone.