RepOD

Here, we investigated genetically engineered E. coli Nissle, improved its adhesion abilities, and enhanced protection against Salmonella infection in in vitro and in vivo models.

This dataset was generated in a study examining how enhanced bacterial adhesion affects intestinal colonization and protection against Salmonella enterica serovar Typhimurium (STm). The study compared the wild-type probiotic strain Escherichia coli Nissle 1917 (EcN^WT) with its mutant variant EcN^G66R, which carries a point mutation in the FimH adhesin and shows markedly stronger adhesion to intestinal epithelial cells.

Two types of sequencing data were deposited:

16S rRNA gene sequencing describes the composition of the bacterial community during probiotic colonization and after Salmonella infection. The dataset includes fecal samples from a colonization experiment in uninfected mice, collected at day 5 of probiotic administration, day 6 (one day after treatment ended), and day 10 (five days after treatment ended), from both EcN^WT and EcN^G66R groups. It also includes fecal samples from a Salmonella challenge experiment, collected at day 5 before infection and at days 1 and 4 post-infection, from the EcN^WT+STm and EcN^G66R+STm groups. In addition, intestinal tissue samples were collected at necropsy on day 6 post-infection from both infected and uninfected probiotic-treated mice. For each group and time point, samples from mice in the same treatment group were pooled prior to DNA extraction, 16S rRNA gene library preparation, and sequencing.

Total RNA sequencing (RNA-seq) describes the host transcriptional response to probiotic treatment and infection, covering two sample types: murine intestinal epithelial cells (MIEC) and mouse spleen tissue. The MIEC samples include untreated cells (M_MIEC), cells exposed to EcN^WT (M_EcN) or EcN^G66R (M_G66R), and cells exposed to each strain together with STm (M_EcN_STm and M_G66R_STm). The spleen samples include tissue from mice treated with EcN^WT (S_ECN) or EcN^G66R (S_G66R), and from mice treated with each strain and then infected with STm (S_ECN_STm and S_G66R_STm). This design allows comparison of the host response between the two probiotic strains, both alone and in the context of Salmonella infection, at the level of the intestinal epithelium and a systemic organ. For each condition, biological replicates were pooled before library preparation and sequencing. The associated analysis covered quality filtering, normalization to transcripts per million (TPM), and identification of differentially expressed genes (DEGs; |log₂FC| > 1, adjusted p < 0.05).