Innate immunity means that it is there right from the very beginning of life. As being essential for the molecular entity of all life, it has to be there otherwise no membrane can be built, can be conserved and make up for an entity that we call life.
The innate immunity is a cross-species phenomenon. The cells of the innate immune system display genetically highly conserved patterns of receptors that can be seen from plants to mammals, patterns and shapes that mirror the structures of bacteria and viruses we live with since thousands and thousands of years. These patterns recognize all bacteria and viruses that live the earth long before humans have populated it.
We are all well equipped to coexist with them, if we didn’t destroy the equlilibrium.
Unfortunately, we ran into serious problems since we use antibiotics without constraints. Under the pressure of the antibiotics the bacteria change genetically and turn ”resistant to antibiotics", fast and change and evasion is their survival strategy.
The innate immune system with its recognition patterns for bacteria has to fail. Changes in men are an incredibly slow process. Bacteria are always a step ahead. But no morals at this point, it simply means that the perfectly adapted innate immunity of ours stayed behind. The bacteria world moved on and changed quickly.
It may as well be that this schism brings about autoimmune diseases that have until lately been well controlled by the harmoniously orchestrated collaboration of bacteria and immune cells. But this is pure speculation from my side, sorry.