On the role of microbial resilience in intestinal inflammation

Loss-of-function variants in the nucleotide-binding oligomerization domain-2 (NOD2) gene, impairing the recognition of the bacterial cell wall component muramyl-dipeptide, are associated with an increased risk for developing Crohn’s disease (CD). A disturbed control of gut microbial communities is hypothesized as a causative mechanism contributing to increased susceptibility for chronic intestinal inflammation through this genetic variation. Here, the influence of NOD2 on the longitudinal dynamics of the intestinal microbiota was demonstrated using wild-type (WT) C57BL/6J and knock-out (KO) NOD2 mice treated with broad-spectrum antibiotics. The microbial community composition was determined by 16S, ITS1, and viral sequencing and the occurrence of antibiotic resistance genes was assessed using qPCR. Antibiotics caused a significant increase in resistance genes and altered the microbial gut community in both genotypes. However, while bacterial diversity decreased, fungal diversity increased, serving as an indicator of gut dysbiosis and impaired host health. Strikingly, the viral community explained 99.2% of the bacterial community variation, and was found to be highly diverse. Interestingly, a significant difference between the genotypes was observed, where the NOD2 genotype impaired bacterial resilience leading to delayed recovery. A delayed resilience was also detected in the virome of both genotypes, whereas, the fungal community remained perturbed. These results demonstrate a complex relationship between gut bacteria, fungi, and viruses, where antibiotic perturbation creates niche availability and the expansion of potentially opportunistic genera. Importantly, NOD2 seems to license resilience of gut microbial communities, as evidenced by the delayed recovery. This may promote colonization with pathobionts and may contribute to the development of chronic intestinal inflammation.


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