Microbes may become pathogenic and mankind develops antimicrobials and vaccines to fight with them, which may lead to an arms race as pathogens develop drug resistance and humans invent newer drugs, often ending up with uncontrollable infections. This book narrates the author’s journey pursuing the origin of pathogenic bacterial species, demonstrating through experiments that bacteria form new species by acquiring novel genes from surroundings and altering the genome for better fitness. If the newly acquired genes encode pathogenic traits, the originally benign bacteria may become new pathogens. To control pathogens, antimicrobials and vaccines are useful in many cases, but, in addition, book proposes a third strategy through the concept of herd resistance via enhancing the protective functions of intestinal microbiota, which will not trigger an arms race nor interfere with immune functions. This strategy can be generalized to a broad range of bacterial or viral pathogens, such as SARS-CoV-2.