GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE343nnn/GSE343117/primaryOK200Othermouse gut metagenomeOtherhttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE343117GEOGSEfalseMining Microbial Transcriptomes to Engineer Cell-Based Bacterial Biosensors in Gut-Resident Bacteroidaceae [BCSeq]The gastrointestinal tract is rich in metabolic, immune, and microbiome-derived signals that can inform the design of live biotherapeutics and diagnosis of intestinal disorders. Engineered cell-based biosensors can tap into this molecular information and report on their environment, yet their development in gut-resident symbionts has been limited by a lack of validated sensor systems. Here, we present a generalizable pipeline that leverages bacterial transcriptional profiling to identify environment-responsive systems for biosensor engineering. Candidate Sensors Systems (CSSs) mined from healthy, disease, and in vitro transcriptomes were assembled into a barcoded library in Bacteroidaceae chassis and screened in high-throughput in vivo to identify responsive promoters. A unique Bacteroidales ECF-type sigma factor operon with ties to sphingolipid metabolism and flux was highly responsive in chemically-induced colitis models. The biosensor responded robustly to disease and returned to baseline upon recovery, establishing an in vivo-driven strategy for discovering functional biosensors in non-model gut-resident bacteria.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 gut metagenome