An effective vaccine for Vibrio choleraeis not yet available for use in the developing world, where the burden of cholera disease is highest. Characterizing the proteins that are expressed by V. cholerae in the human host environment may provide insight into the pathogenesis of cholera and assist with the development of an improved vaccine. We analyzed the V. cholerae proteins present in the stools of 32 patients with clinical cholera. The V. cholerae outer membrane porin, OmpU, was identified in all of the human stool samples, and many V. cholerae proteins were repeatedly identified in separate patient samples. The majority of V. cholerae proteins identified in human stool are involved in protein synthesis and energy metabolism. A number of proteins involved in the pathogenesis of cholera, including the A and B subunits of cholera toxin and the toxincoregulated pilus, were identified in human stool. In a subset of stool specimens, we also assessed which in vivo expressed V. cholerae proteins were recognized uniquely by convalescent-phase as opposed to acute-phase serum from cholera patients. We identified a number of these in vivo expressed proteins as immunogenic during human infection. To our knowledge, this is the first characterization of the proteome of a pathogenic bacteria recovered from a natural host.Vibrio cholerae is a gram-negative bacillus that exists within an aquatic reservoir and that can cause severe, dehydrating, and occasionally fatal diarrhea in humans (11). Strains of V. cholerae are differentiated serologically by the O side chain of lipopolysaccharide, and the majority of toxigenic strains belong to serogroup O1 or O139. V. cholerae O1 occurs in two biotypes, classical and El Tor, which differ in biochemical characteristics and phage susceptibility. Since 1817, there have been seven cholera pandemics during which disease has spread from the Indian subcontinent across Asia, Europe, Africa, and the Western Hemisphere. The disease is also endemic in floodprone regions of South Asia, such as Bangladesh, where seasonal outbreaks typically occur in the spring and fall. The ongoing seventh pandemic of cholera is due to the O1 El Tor biotype of V. cholerae, and more than 100,000 diarrheal deaths per year are attributed to infection with this organism. Although a number of cholera vaccines have been developed over the past 100 years, an effective vaccine is not yet available for use in the developing world, where the burden of disease is highest (21).Humans are the only known host and reservoir for V. cholerae outside its aquatic environment, and an important limitation to the development and testing of cholera vaccines has been the lack of an optimal animal model of infection. It is consequently of great interest to understand which virulence factors are expressed by the organism directly in the human host environment, since in vivo expressed antigens of V. cholerae may represent targets of protective human immune responses. The capacity to perform such research has been facilitated by the sequen...