Penicillin, and its deadly poisonous antibiotic cousins, kill billions of life forms yearly. Some near-extinct critters hardly exist, these days, outside the zoos of biologists' labs. The little Anthrax critter, for example, and variola.
These little bugs are just as much a part of the ecosystem as any other living thing.
Photo is of the Pneumococcus, a species which humans attack and kill by the billions every year. Even good old treponema pallidum and yersinia pestis are near extinction.
Where is PETA? This is a serious biodiversity issue. The vast majority of earthly life forms require microscopes to see, but is that any reason to excuse man-made extinction of these critters?
Is it just because they don't look cuddly? Dr. William Osler famously termed pneumoccal pneumonia "the old man's friend" because it provided a peaceful ending.