Mycobacterium bovis BCG, the only presently available vaccine against tuberculosis, was obtained from virulent M. bovis after serial passages in vitro. The vaccine strain retained at least some of its original virulence, as it persists in immune-competent hosts and occasionally may cause fatal disease in immunedeficient hosts. Mycobacterial persistence in vivo is thought to depend on anaerobic metabolism, an apparent paradox since all mycobacteria are obligate aerobes. Here we report that M. bovis BCG lacking anaerobic nitrate reductase (NarGHJI), an enzyme essential for nitrate respiration, failed to persist in the lungs, liver, and kidneys of immune-competent (BALB/c) mice. In immune-deficient (SCID) mice, however, bacilli caused chronic infection despite disruption of narG, even if growth of the mutant was severely impaired in lungs, liver, and kidneys. Persistence and growth of BCG in the spleens of either mouse strain appeared largely unaffected by lack of anaerobic nitrate reductase, indicating that the role of the enzyme in pathogenesis is tissue specific. These data suggest first that anaerobic nitrate reduction is essential for metabolism of M. bovis BCG in immune-competent but not immune-deficient mice and second that its role in mycobacterial disease is tissue specific, both of which are observations with important implications for pathogenesis of mycobacteria and vaccine development.Mycobacterium tuberculosis claims more human lives each year than any other bacterial pathogen. Mycobacterium bovis BCG, the only presently available vaccine against tuberculosis, belongs phylogenetically to the M. tuberculosis complex. In humans, M. bovis BCG, like M. tuberculosis, forms granulomas and abscesses in various tissues. Following vaccination in immune-competent individuals, M. bovis BCG may persist for extended periods (34). In immune-compromised individuals the vaccine strain may even lead to fatal disease (2,3,10,11,14,21,27,30,36,39).Mycobacteria become firmly established within host tissues, adapting their metabolism to the available source of carbohydrates, nitrogen, and energy (4). Although the acquisition of essential nutrients by mycobacteria is an area of considerable interest, our knowledge of bacterial metabolism throughout the course of infection remains rudimentary. A recent study revealed that metabolism of fatty acids serves as a source of carbohydrates and is required for persistence of M. tuberculosis in mice and activated macrophages (25). Nitrate, through nitrate respiration, could provide energy for bacterial metabolism in an anaerobic environment, because anaerobic nitrate reductase (NarGHJI) couples the reduction of nitrate (NO 3 ) to the generation of ATP by replacing oxygen as a terminal electron acceptor (29). Anaerobic nitrate reductase coding sequences (narGHJI) have been identified in both obligate aerobes such as Bacillus and Pseudomonas and facultative anaerobes such as Escherichia coli (5, 17, 28). However, a role of this enzyme in virulence was not established. In mycobacteria,...