Take a look at this today's BBC "Future" feature on cleanliness and the hygiene hypothesis just published on their website. It's well worth a read and a “first” i.e an attempt to set concern about microbe exposure and allergies against the need for hygiene – in the same article.
On one hand it’s very informative – but there are also some misleading quotes which shows we still have a long way to go to get public understanding. Although it talks well and in some detail about all the reasons why we may have lost exposure to the vital microbes needed to prevent our immune system overreacting to allergens, the main message that still comes over is that “over cleanliness is the main problem”. It uses the term "cleanliness" as the generic term for loss of exposure to microbes regardless of whether this means i.e C- section instead of natural childbirth, bottle instead of breast feeding – or overuse of antibiotics, none of which could really be regarded as “cleanliness”
The final message readers are left with is that infectious illness make the immune system stronger. The final para says "On the plus side, you can take heart in knowing that every time you get a little sick, you get a little stronger. “The message is not one that most people want to hear: they want the quick pharmaceutical fix for the slightest bit of discomfort. But every time you take the quick fix, you make your body a little weaker.” That’s something to remember the next time you’re tempted to slather on the shower gel". Very confusing since this is not what the article is about
The article is at http://www.bbc.com/future/story/20151118-can-you-be-too-clean.