Is there clear evidence for the hygiene hypothesis?

There is clear evidence for the hygiene hypothesis. 

For example, studies have demonstrated increased asthma in genetically similar populations in which one population farms in an old fashioned and "dirtier" environment while the other population uses modern and "cleaner" farming methods. The cleaner population had a significantly increased frequency of asthma, suggesting that exposure to bacterial products in the dirtier environment "educates" and "acclimates" and essentially calms the immune system to environmental and self-stimuli, - so there is less of an over-reponse to both environmental and self stimuli (and less asthma). In the "cleaner" and more asthmatic environment, direct evidence was documented showing that the immune system over-reacts to such stimuli.  (Stein, M.M., et. al., 2016. N Engl J Med 375: 411-421. "Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children").

The mechanism underlying this concept was also clearly modeled in a mouse model (Schuijs,M.J. et.al., 2015. Science 349:1106-1110. "Farm dust and endotoxin protect against allergy through A20 induction in lung epithelial cells)).