{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE343nnn/GSE343114/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Bacteroides thetaiotaomicron"," mouse gut metagenome"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE343114"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Mining Microbial Transcriptomes to Engineer Cell-Based Bacterial Biosensors in Gut-Resident Bacteroidaceae [DSS RNAseq]","description":"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.","dates":{"publication":"2026/08/24"},"accession":"GSE343114","cross_references":{"GSM":["GSM9946280","GSM9946287","GSM9946288","GSM9946285","GSM9946286","GSM9946283","GSM9946284","GSM9946281","GSM9946282","GSM9946269","GSM9946267","GSM9946289","GSM9946268","GSM9946290","GSM9946291","GSM9946276","GSM9946277","GSM9946274","GSM9946275","GSM9946294","GSM9946272","GSM9946273","GSM9946295","GSM9946270","GSM9946292","GSM9946293","GSM9946271","GSM9946278","GSM9946279"],"GPL":["37350","37336"],"GSE":["343114"],"taxon":["Bacteroides thetaiotaomicron"," mouse gut metagenome"]}}