There are many human behaviors that can decrease overall exposure to microbes, most of which have to do with hygiene.
The increased number and frequency of usage of cleaning products in the modern home have contributed to lower exposure to microbes, especially decreasing the variety of microbes that people experience. The household areas will get reseeded with microbes that are already in the house, such as those from the people living inside.
On the same topic, the increased frequency of bathing over the centuries have contributed to decreased microbiome exposure. Showers essentially wipe out the skin microbiome due to the soap, the high heat, and the friction of the water. This can also decrease the variety of microbial exposure, as odd microbes from the outside will get washed away in the shower before they can take hold.
Speaking of the outside, the tendency in the modern era to stay inside, especially in hotter areas, decreases the exposure to new microbes that would help to develop the immune system. additionally, modernity has allowed more and more people access to air conditioning, which limits the amount of time that windows stay open, thus further limiting the amount of outside exposure that buildings have.
Lastly, there is also a trend over the past few millennia towards more and more cooked foods as opposed to raw foods. This is overall a good thing, as it has decreased the amounts of food borne illnesses, but it has also decreased the amount of commensal microbes that people are exposed to in foods. Probiotics and the raw food diet have attempted to somewhat remedy these issues, but they have yet to grow in popularity enough to fully make up for it.
