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Abstract:
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. The presence of virus-like particles was also identified by transmission electron microscopy, and the occurrence of antibiotic resistance genes was assessed using qPCR. Additionally, since intestinal secretory immunoglobulin A (SIgA) is important in the regulation of the bacterial community, IgA levels were determined across different genotypes of both wild and lab mice to assess whether a pattern could be detected.
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, composed predominantly of bacteriophages, and a low abundance of eukaryotic viruses. 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. A pattern of IgA levels was not detected in the wild mice; however, a significant difference across time was observed in the ATG16L1 lab
mice, where IgA levels increased as mice aged. Moreover, a significant difference was also observed when comparing male wild mice with male lab mice where higher IgA levels were found in the wild mice.
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.
