A wild hypothesis here. One thing I noticed in "pre-Western" diets that's absent from modern ones is unpasteurized dairy. All milk sold in Western countries is pasteurized (treated thermally to kill most of its bacteria). If you leave on a shelf, it will remain unspoiled for quite a long time compared to unpasteurized, but when it does spoil, it becomes completely undrinkable, with foul smell. Unpasteurized milk, on the other hand, has a much shorter shelf life, however the spoiled product is acidic and yogurt-like, has no foul smell, and is (mostly) safe to consume, even by people with some degree of lactose intolerance (it has had most of its lactose converted to lactic acid, hence the sour taste). This so-called Soured milk (https://en.wikipedia.org/wiki/Soured_milk) is extremely commonly consumed in many Eastern European countries that don't have Western food safety standards.

While there may be other beneficial (to the immune system) things happening in Russian Karelia, I can't help but wonder if the absence of unpasteurized dairy is the single massive thing that causes failure of gut microbiomes in the modern world.