Non invasive assessment of gut function with transcriptional recording sentinel cells

We use Record-seq enabled E.coli as sentinel cells in the mammalian gastrointestinal tract. These sentinels, when recovered from the feces, report on the host intestinal environment, including alterations in the host diet, induced inflammation, and microbiome complexity. In addition to this, we also report increased efficiency of Record-seq and demonstrate multiplexed recordings, , facilitating reconstruction of transcriptional histories of different strains within a single taxon.