RDA for microbes — are you getting your daily dose?

For almost all of human evolution our food and water has contained large numbers of microbes. Our immune systems evolved to cope with this daily intake, and our microbiomes (the collection of microbes on and in the human body) are increasingly recognized as playing an important role in human health. However, in recent times we have gone to great lengths to eliminate microbes from our diets, using food processing, water purification and hygiene to reduce our exposure. But has this come at a cost? Could our immune systems, primed to deal with trillions of microbes with every meal, be struggling to cope with their absence? Could this be a factor in the rise of modern inflammatory diseases in which the immune system misbehaves in response to dietary antigens or to our own epithelial cells? Perhaps we need to go back to consuming large numbers of (safe) microbes every day — a microbial RDA?