The focus of research concerning human pathogens has been primarily centered on virulence in the host, transmission between hosts, and treatment of the subsequent infections. Justifiably, our well-being relies on such research but it has erroneously resulted in the assumption that the role of these microbial pathogens is to infect and reproduce within or on our bodies and then pass to another human to follow this same cycle ad infinitum. Although this does represent a true optional lifestyle for many pathogens, it must be stated that this lifestyle is one of several life histories that a pathogen may follow and in many cases human infections represent a dead end. This study focuses on the natural ecology of several human pathogens, V. cholerae, V. parahaemolyticus, and V. metecus, and their associated virulence factors, in regions where they cause sporadic illness as well as a region where one of these pathogens, V. cholerae, has never caused a human illness. In this work we demonstrate the non-human environment as a natural ecosystem for several human pathogens as well as a reservoir of virulence factors. This was achieved by employing a combination of high-throughput whole genome analyses focused on the nucleotide and amino acid level, combined with broader ecological studies evaluating the role of the environment with respect to presence of the pathogens and expression of their virulence factors. This work further demonstrates the ubiquity of virulence factors in the environment and the expression of these factors at temperatures found outside of the human host suggests their utility in the environment.