Imprinting of the neonatal gut epithelium by flagellated commensal bacteria

Imprinting of the neonatal gut epithelium by flagellated commensal bacteriaThe neonatal period is essential for the establishment of microbiota-host interactions, as the gut microbiota influences immune responses with life-long consequences. However, mechanistic understanding of the underlying processes is incomplete. We used a gnotobiotic approach combined with multi-omics sequencing to study the effects of flagellated bacteria on microbiota development. Germfree mice were colonized with nine non-flagellated bacterial strains and either with the flagellated E. coli strain DSM112117 or its non-flagellated isogenic mutant delta-fliC. Imprinting of the customized microbial communities on the small intestinal epithelium was studied in gnotobiotic offspring at 7 days of age using single-cell RNA sequencing (scRNA-Seq) and 16S rRNA gene amplicon sequencing.