Pathogenesis hinges on successful colonization of the gastrointestinal (GI) tract by pathogenic facultative anaer-obes. The GI tract is a carbohydrate-limited environment with varying oxygen availability and oxidoreduction potential (ORP). How pathogenic bacteria are able to adapt and grow in these varying conditions remains a key fundamental question. Here, we designed a system biology-inspired approach to pinpoint the key regulators allowing Bacillus cereus to survive and grow efficiently under low ORP anoxic conditions mimicking those encountered in the intestinal lumen. We assessed the proteome components using high throughput nanoLC-MS/MS techniques, reconstituted the main metabolic circuits, constructed ⌬ohrA and ⌬ohrR mutants, and analyzed the impacts of ohrA and ohrR disruptions by a novel round of shotgun proteomics. Our study revealed that OhrR and OhrA are crucial to the successful adaptation of B. cereus to the GI tract environment. Specifically, we showed that B. cereus restricts its fermentative growth under low ORP anaero-biosis and sustains efficient aerobic respiratory metabolism , motility, and stress response via OhrRA-dependent proteome remodeling. Finally, our results introduced a new adaptive strategy where facultative anaerobes prefer to restrict their fermentative potential for a long term benefit. Molecular & Cellular Proteomics 11: 10.1074/ mcp.M111.013102, 1–13, 2012. Facultative anaerobes encompass all the major pathogens of the human gastrointestinal (GI) 1 tract. The GI tract poses several challenges for pathogens because it is sliced into distinct niches with different oxygen concentrations and different oxidoreduction potentials (ORP) (1–3). Although much is known about gene expression and metabolism under fully aerobic and high ORP anaerobic condition (4, 5), our knowledge about the physiological impact of low ORP anoxic conditions and the underlying molecular mechanisms is scarce (6). Bacillus cereus is a notorious food-borne pathogenic bacterium. Like the closely related Bacillus anthracis (7, 8), it is a recognized agent of GI tract infections (9 –11). The critical step of infection takes place in the small intestine, where B. cereus has to grow and produce virulence factors to induce diarrheal disease (11, 12). Thus, how B. cereus adapts its catabolism and regulates its proteome across the range of physiologically relevant ORP and oxygen availabilities is important for its survival and growth. In B. cereus, anaerobic and aerobic catabolism work through different pathways. In the presence of oxygen, reducing equivalents generated by glycolysis and the TCA cycle (NADH and FADH) are reoxidized by the respiratory chain, resulting in the buildup of a proton motive force and the subsequent synthesis of ATP. Acetate excretion can occur aerobically when carbon flux into the cells exceeds TCA cycle capacity. In the absence of oxygen or other external electron acceptors (such as nitrate), NADH is reoxidized in terminal step fermentative reactions from pyruvate. When grown in pH-controlled anaerobic batch cultures (pH ϳ7), the fermentative by-products of B. cereus are lactate, succinate, acetate, and ethanol. The relative rate of formation of these products is influenced by the ORP of the growth medium, which directly impacts the intracellular redox state (6, 13–18). The intracellular redox state is dependent on the degree of oxidation or reduction of various redox-active species. Among these species, NAD(P)H/NAD(P) and low molecular weight thiol/disulfide (SH/S-S) compounds are of special significance because they mediate redox regulation through direct effects on proteins. The activities of many metabolic enzymes depend on the steady-state NAD(P)H/NAD(P) ratio, whereas proteins with essential SH/S-S groups can be regulated by post-translational modification involving cellular thi-ols and disulfides. The main low molecular weight thiols in B. cereus ATCC 14579 cells are bacillithiol and cysteine (19). On the other hand, the NAD(P)H/NAD(P) and SH/S-S ratios are closely related to cellular levels of reactive oxygen species (ROS). NAD(P)H and thiols contribute to ROS formation via