I suspect the answer has to do with the microbiome and its cumulative response over decades to antibiotics and tiny changes introduced in food (shifts in cookin

I suspect the answer has to do with the microbiome and its cumulative response over decades to antibiotics and tiny changes introduced in food (shifts in cooking oils, dairy product additives, even animal feed that then indirectly impacts our own microbiome when we eat meat or eggs or dairy, etc.). The problem is that studies on the microbiome tend to be limited and recent. Long-term studies are especially lacking. What we do have indicates the microbiome may be vital to not just digestion but also our immune system function, emotional well-being and weight. Probiotics might be helpful here, but in no way are we close to an exact science on the microbiome.