While decay and germs are sometimes the cause of diseases and other negative impacts on the earth, some of this kind of cellular breakdown is necessary. It would not be possible to have yogurt, cheese or even beer if plants and other materials could don't decay and ferment. When dead plants and animals get broken down by microbes, nutrients are returned to the soil to enrich it so more plants can grow. Without this cycle, humans and animals would die from a lack of food.
Microbes deep in the ocean are also necessary for keeping the planet breathing. Phytoplankton in the oceans are what produces more than half of the oxygen on the planet. In addition to the microbes all around us, our bodies carry thousands of kinds of bacteria and most of those serve a purpose to digest food and break down toxins. While the harmful disease causing bacteria in the world is a problem, there are far more helpful microbes that are necessary for life.