I've read/heard some discussion about how humans suffer detriment now that we no longer have gut parasites living with us. Unfortuntely it's been rather thin on the ground, I suppose it's not a very glamourous area to study.
We are rapidly approaching an era of medical treatments where giving a treatment of "probiotics" to correct your newborn child's gut bacteria in order to prevent asthma much the way we give immunisations against diseases today. The hygiene hypothesis is getting some pretty compelling evidence and hopefully it will lead to us learning the "right" kind of things we should be exposing our children to in order to prevent these autoimmune conditions.
> In the pre-epidemic era, enteric infections were so ubiquitous that most infants were infected within 6–12 months, at a time when they had circulating antibodies passively derived from their nursing mothers. Although serum antibodies did not prevent enteric infection, they were sufficient to preclude viremia, thereby avoiding invasion of the central nervous system and paralysis. The result was the acquisition of active immunity under the cover of passive protection.
So the hypothesis is that historically most people did have it and were immune, and only the improved hygiene past 1900 led to epidemics. We can indeed ask whether some individuals are worse off now because they didn't contract it in their infancy. But we're also doing pretty much the same thing with the vaccinations. Maybe we'll see a rise in allergic reactions when polio 2 vaccines are phased out. I don't think that anybody would advise infecting babies to get the benefits back though :-)