I am going to provide an example using raw milk. You may not like milk, you may not think people should drink milk, it may even be against your religion. None of that is being challenged here. This writing isn’t meant to convince you to drink milk. It is just an example of the faulty information being presented by an organization that is supposed to protect us and promote our health.
Raw milk is to be avoided by pregnant mothers (according to the USDA) because you may contract an infection from Listeria monocytogenes, which is a food-borne pathogen. This infection can be serious, especially to the neonate. This sounds like good advice, but if you dig into this, you will identify substantial bias in the information they provide. According to a report issued by the USDA and FDA in the early 2000s, there were 29 times more cases of Listeria infection from pasteurized milk than from raw milk—and pasteurized milk carries no warning from the USDA. Another comparison, to demonstrate biases in their information, can be made using deli meats. You are ten times more likely to contract an infection from Listeria consuming a serving of deli meats than a serving of raw milk, though deli meats are not stated as foods to avoid by the USDA, merely as foods to be careful with.
For those of you who do drink milk, you should consider the differences between raw and processed milk. Pasteurization destroys some of the nutrition found in milk and damages the milk protein so that calcium becomes less bioavailable (calcium is one of the main reasons many people drink milk—but pasteurization means you get less calcium from this processed food). In fact, processed milk contains 1/2 to 1/6 the bioavailable minerals as raw milk. Homogenization, believe it or not, also alters this food, stripping away a lipid membrane and causing your body to fail to recognize milk as food (i.e., it sees it as an allergen). If you do drink milk, I would highly recommend only raw milk from primarily grass-fed cows, avoiding Holstein breeds if possible (there is a long discussion here as to why). If you are concerned about nourishing your unborn child, there is every reason to consider raw dairy as superior to processed dairy (i.e., there is every reason to not follow the USDA’s recommendations).
If you are grossed out by the thought of raw milk, please consider this: pasteurized milk is not sterile, it will still become putrid even if it is not opened. Pasteurization kills the beneficial bacteria (but not the putrefying ones), so that when processed milk is days past its due date, it is truly disgusting. We routinely keep raw milk in our home for weeks past its due date. At that time, it has become too sour to enjoy as a beverage, but is still perfectly safe to use in baking (it is sour due to an abundance of safe bacteria). And remember, there are several traditional groups of people who enjoyed long, healthy lives using raw dairy as a staple. Said another way, there is historical information that shows people can consume the milk of other animal species and prosper, so long as the animals are fed biologically appropriate food and the milk is not processed using pasteurization and homogenization.