Disruption of the primocolonizing microbiota alters epithelial homeostasis and imprints stem cells in the colon of neonatal piglets

Abstract

The gut microbiota plays a key role in the postnatal development of the intestinal epithelium. However, the bacterial members of the primocolonizing microbiota driving these effects are not fully identified and the mechanisms underlying their long‐term influence on epithelial homeostasis remain poorly described. Here, we used a model of newborn piglets treated during the first week of life with the antibiotic colistin in order to deplete specific gram‐negative bacteria that are transiently dominant in the neonatal gut microbiota. Colistin depleted Proteobacteria and Fusobacteriota from the neonatal colon microbiota, reduced the bacterial predicted capacity to synthetize lipopolysaccharide (LPS), and increased the concentration of succinate in the colon. The colistin‐induced disruption of the primocolonizing microbiota was associated with altered gene expression in the colon epithelium including a reduction of toll‐like receptor 4 (TLR4) and lysozyme (LYZ). Our data obtained in porcine colonic organoid cell monolayers suggested that these effects were not driven by the variation of succinate or LPS levels nor by a direct effect of colistin on epithelial cells. The disruption of the primocolonizing microbiota imprinted colon epithelial stem cells since the expression of TLR4 and LYZ remained lower in organoids derived from colistin‐treated piglet colonic crypts after several passages when compared to control piglets. Finally, the stable imprinting of LYZ in colon organoids was independent of the H3K4me3 level in its transcription start site. Altogether, our results show that disruption of the primocolonizing gut microbiota alters epithelial innate immunity in the colon and imprints stem cells, which could have long‐term consequences for gut health.

Initial pig developmental stage influences intestinal organoid growth but not phenotype

“…Beside weaning, the neonatal period (from birth to post-natal day 28 in pigs), is also a key period in terms of intestinal development, with changes in epithelium morphology and gene expression with post-natal age [13], as well as ISC dynamics depending on gut location [14]. As opposed to weaning where the luminal environment does not seem to impact ISC, we recently demonstrated that changes in the luminal environment composition during the first week of life can imprint ISC, since organoids derived from the colon of antibiotic-treated vs. vehicle-treated piglets retained some, but not all, features of the changes observed in vivo at the epithelial level [15].…”