Gene expression profiles of E. coli in the gut of inflammatory bowel disease models.

Gut microbiota modulation has emerged as a potential therapeutic and diagnostic approach for inflammatory bowel disease (IBD). We generated transcriptomic data by Record-seq, a method based on CRISPR-Cas system, that enables recording of gene expression in reporter bacteria within the mouse gut. IBD was induced in male C57BL/6 mice by DSS or DNBS administration. Additionally, feed containing Lactobacillus crispatus was provided to the mice to modulate the gut microbiota. For record sequencing, we utilized Escherichia coli BL21(de3) transformed with pFS_0453 plasmid containing a CRISPR array. Plasmid-derived spacer libraries were constructed according to original Record-seq protocol and sequenced on a Illumina NovaSeq X Plus platform.