Manure can contain pathogens that contaminate the food. Unless it is processed properly to kill off pathogens, its use on food crops is unsafe.
On the surface, this seems more a USDA matter than FDA.
NOW they are worried about the effects of manure on the environment?
Where have these people been? Certainly very few, if any, were ever raised in the country, or with some kind of pet around the house if they were urban or even suburban. It is not only cows and horses, but dogs, cats, and birds that drop excrement everywhere they go, and a major part of animal husbandry every day is collecting and disposing of fecal matter.
It can be composted, yes, but that is generally a rather slow process, and requires some sort of facilities where it may be contained until the composting is completed (which totally destroys most pathogens, by the way). Or it may be aerated, which gets rid of most of the volatiles, especially moisture, without which the pathogens (and most other microbiota) quickly die or go form spores. Spreading thinly on areas exposed to the sunlight is DEADLY for these same pathogens, so surface land disposal is in fact a rather hygienic method of disposal. Methane release is not, and never was, the bugaboo of atmospheric “pollution” it has been made out to be. Lighter than the normal mix of atmospheric gases, it rises quickly in the atmosphere, and is destroyed by the ionization of oxygen by sunlight, which in turn produces carbon dioxide and water from the methane.
Most of the rest of animal excrement is composed of some form of fiber, and nitrogenous material from digestion of protein, both of which combine with the existing soil structure to create a condition known as “tilth”, the effective separation of the mineral proportion of soil by the introduction of a non-crystalline structure, which makes it much simpler to cultivate and plant desirable crops. By incorporating this animal waste into the upper layer of topsoil, the fertility of a plot of land is preserved for all time.
Naturally occurring bacterial life in the soil also goes far to control or even eliminate what few pathogens remain in the now composted, aerated and irradiated fecal matter, and so long as crops are not sprayed with liquid fecal matter shortly before harvest, the consumption of these crops is about as safe as anyone can guarantee anything in nature.