Early-Life Microbial Restitution Reduces Colitis Risk Promoted by Antibiotic-Induced Gut Dysbiosis in Interleukin 10–/– Mice

Background & Aims Perturbations in the early-life gut microbiome are associated with increased risk for complex immune disorders like inflammatory bowel diseases. We previously showed that maternal antibiotic-induced gut dysbiosis vertically transmitted to offspring increases experimental colitis risk in interleukin (IL) 10 gene deficient (IL10–/–) mice, a finding that may result from the loss/lack of essential microbes needed for appropriate immunologic education early in life. Here, we aimed to identify key microbes required for proper development of the early-life gut microbiome that decrease colitis risk in genetically susceptible animals. Methods Metagenomic sequencing followed by reconstruction of metagenome-assembled genomes was performed on fecal samples of IL10–/– mice with and without antibiotic-induced dysbiosis to identify potential missing microbial members needed for immunologic education. One high-value target strain was then engrafted early and/or late into the gut microbiomes of IL10–/– mice with antibiotic-induced dysbiosis. Results Early-, but not late-, life engraftment of a single dominant Bacteroides strain of non–antibiotic-treated IL10–/– mice was sufficient to restore the development of the gut microbiome, promote immune tolerance, and prevent colitis in IL10–/– mice that had antibiotic-induced dysbiosis. Conclusions Restitution of a keystone microbial strain missing in the early-life antibiotic-induced gut dysbiosis results in recovery of the microbiome, proper development of immune tolerance, and reduced risk for colitis in genetically prone hosts.