![]() coli from records of uptake and metabolism of fiber-derived saccharides liberated by B. Cocolonization with Bacteroides thetaiotaomicron revealed likely cross-feeding of E. ![]() In a dextran sulfate sodium (DSS) colitis model, sentinel cells recorded transcriptional alterations consistent with reduced anaerobic metabolism, a stringent response, and increased oxidative and membrane stress. ![]() In addition to information about carbon source preference and metabolism, the transcriptome-scale records also provided evidence of an acid-stress response that was associated with a lowered pH in the cecum of starch-fed mice. coli and a ∆ idnK/∆ gntK mutant defective in hexuronate catabolism. This included evidence of different carbon source preferences and bacterial hexuronate metabolism through the Entner-Doudoroff pathway under conditions of restricted carbon source availability, which was then verified through competitive colonization of wild-type (WT) E. Direct measurements showed that Record-seq efficiently captured proximal transient transcriptional events. Transcriptional records of these diets were preserved in fecal spacer sequences even 2 weeks after a dietary switch, whereas diet-specific fecal bacterial RNA-sequencing (RNA-seq) profiles were rapidly lost. Fecal Record-seq profiles were distinct for mice on chow diet versus starch or fat diets. Sentinel cells retrieved from feces of stably colonized germ-free mice accumulated new spacers over time and during intestinal transit. ![]()
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