DOP37 Noninvasive assessment of gut function using transcriptional recording sentinel cells

Abstract

Abstract Background Bacteria within the human gut continuously adapt their gene expression to environmental conditions that are associated with diet, health, and disease. Noninvasive measurements of bacterial gene expression patterns throughout the intestine are important to understand in vivo microbiota physiology and pathophysiology. Current methods do not offer sufficient information about transient or proximal events within the intestine without using indirect or invasive approaches that disturb normal physiology and are inapplicable to clinical practice. Methods Here we used transcriptional recording sentinel cells that through a reverse transcriptase-Cas1–Cas2 complex record their own short-lived mRNA expression into long-lived DNA-based CRISPR arrays to report on gut function. We colonized gnotobiotic mice with E. coli sentinel cells and performed Record-seq on fecal samples to reconstruct their cellular histories as they passed along the gastrointestinal tract. Results Upon colonization of the mouse intestine, sentinel cells reported on diet, inflammation, and microbial interactions. Through transcriptome-scale information, Record-seq elucidated E. coli’s adaptations to intraluminal conditions including pH, oxygen levels, and ion availability. Unlike RNA-seq, Record-seq performed on stool samples retained information from proximal gut sections to noninvasively report on the luminal conditions in vivo. In a mouse model of inflammatory bowel disease, Record-seq not only diagnosed the inflammation in a severity-dependent manner but also revealed pathological gut conditions such as mucus depletion and hyperoxygenation. Conclusion Transcriptional recording sentinel cells noninvasively report on gut function and reveal environmental cues such as diet, inflammation, and microbial interactions, even in proximal gut sections that are otherwise unamenable to unbiased diagnostic interrogation.