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Discoveries by scientists like Antonie van Leeuwenhoek and Robert Koch connected microbes to infectious disease. These discoveries formed a way of thinking called “germ theory” that said a specific microbe caused a specific disease. With widespread use of antibiotics beginning in the 1940s, people zealously tried to rid their lives of any and all microbes, spreading the anti-microbial mindset to personal and household cleaning.

But today, scientists are starting to reevaluate germ theory. Using antibiotics to treat bad germs will remain an essential, life-saving part of medicine. But repeated or unnecessary use of antibiotics prevents our bodies from establishing the community of microbes it needs. Scientists now suggest that we look at microbes in context, understanding that microbes (Helicobacter pylori, for example) can be both beneficial and harmful

Overusing antibiotics has pushed microbes to evolve resistance, making them less available for general health care or surgical procedures. Clostridium difficile (pictured) is an example of a strongly antibiotic-resistant microbe. Successful treatment of C. diff. happens when a patient’s gut community comes back into balance, often by introducing a new microbial community from the stool of a healthy donor.