We really don't know - but I really think there is a link between gut bacteria and allergies, based on some of the reading I've done, though it's all very early days for research in this area. Our boy has allergies and we've been giving him Water Kefir daily for the last year (we would give Milk Kefir, but he's currently allergic to dairy too :(
His allergies developed after a dose of antibiotics - which likely would have wiped his gut bacteria out, so anything which can help him there is worth trying. The amount he's had now though, it's be shocked if he wasn't better than average in that metric
I personally think that we will look back at the symbiotic relationships that bacteria provide, and be amazed by the way we currently live - with hand sanitisers, and even antibiotic dish soap - plus antibiotics in our meat and water... Sure we will look back on this time in the same way we look at Romans and lead water pipes.