> Those "natural" toxic substances have been around long enough to have been
> proven by millions of years and millions of encounters to not be the cause
> of a ubiquitous problem.

We don't know the effect of toxins on species millions of years ago. Presumably many species were wiped out by natural toxins. The natural toxins produced by a variety of bacteria. For example, they cause larval death in the case of American Foulbrood. 

> In the mid to late stage of the P. larvae infection cycle, bacteria circulate in bee hemolymph which contains hemocytes. Hemolysins are a class of bacterial toxins with lytic activity against blood cells. Damage to the host is likely the result of mixed effects from the hemolysins and toxins that can be encoded by P. larvae. Its ability to survive in the host by evading the immune system, as well as protecting itself against other gut bacteria, is likely made possible due to the antibiotic proteins that may be expressed.

It is especially important to note that bacteria can evolve to evade the host defenses, and become more toxic. Chemicals can't do this, although chemists can.

P

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