Impact of microencapsulation on E. coli transcriptome under simulated gastric stress: Implications for oral fecal microbiota transplant delivery

• Chitosan-genipin microencapsulation enhances oral FMT. • Superior protection against gastric acid. • Maintains bacterial viability and function. • Promising non-invasive treatment. Fecal microbiota transplantation (FMT) constitutes a practical therapeutic approach for a range of gastrointestinal disorders; nonetheless, its predominant delivery method, colonoscopy, limits its broader application adoption. Oral FMT offers a less invasive alternative, but the harsh gastric environment necessitates a protective delivery system. This research investigated how well microencapsulation with chitosan and chitosan-genipin safeguards Escherichia coli in conditions that simulate gastric transit. Microfluidic encapsulation generated uniform microcapsules, and simulated gastrointestinal analysis revealed superior stability for chitosan-genipin over chitosan alone. RNA sequencing and bioinformatics showed that chitosan-genipin significantly reduced simulated gastric fluid-induced transcriptomic disturbances in E. coli , lowering differentially expressed genes compared to chitosan or non-encapsulated samples controls. These findings suggest chitosan-genipin microencapsulation is a promising method for non-invasive and effective oral fecal microbiota transplant delivery.