Mouse study highlights role of NOD2 gene in gut microbiota resilience following antibiotics

New investigations using a gene knockout mouse model showed that neonatal exposure to antibiotics had a long-lasting effect on both the microbial community and mucosal immunity in the gut. The data also shone light on how the Nod2 gene alters the risk of inflammatory disease.

The neonatal period is a known critical window during which microbiota colonizes the gut and influences the development of the mucosal immune system. During this period, the developmental processes of the gut microbiome and immune system are particularly sensitive to environmental disturbances, which can increase the susceptibility of an individual to certain diseases.

One well-documented environmental exposure is antibiotics. Both mouse and human studies have produced data that suggest neonatal exposure to antibiotics is associated with increased risks for inflammatory diseases like asthma or inflammatory bowel disease (IBD)— including Crohn’s and ulcerative colitis. Observational data also support the notion that early and repeated exposure to antibiotics significantly increases the risk of IBD.

However, in most immune related or inflammatory diseases, there is likely to be an interplay of environmental and genetic risk factors that lead to someone developing an inflammatory condition. One of the most important genetic risk factors for the development of Crohn’s disease, for example, is mutations in the Nod2 gene. This gene encodes for a protein that has an important role in immune function and is found immune system cells like monocytes, macrophages, and dendritic cells. Nod2 is therefore an interesting candidate for studies aimed a better understanding the role of host genetics in altering the varied and potentially long-lasting effects of antibiotic exposure and risks of inflammatory diseases.

The existence of a mouse breed without the Nod2 gene provided a team of researchers with the ideal model to investigate how Nod2 deficiency influenced the impact of antibiotic exposure on the mouse’s gut microbiota and susceptibility to colitis. The team, based at the University of Toronto and Mount Sinai Hospital in Toronto, included Dr.Kenneth Croitoru (a Microbiome Insights scientific advisory board member). Together with collaborators, Croitoru performed several experiments whereby wild type mice, those with unaltered Nod2 genes, and Nod2 knockouts (mice without any copies of the gene) were exposed to antibiotics.

In a set of experiments, the team gave both adult mice and neonates a treatment of antibiotics, and 5 weeks later experimentally induced colitis. They collected fecal samples from the mice in order to characterize the changes to the gut microbiota using 16S rRNA sequencing. The results showed that in adult mice the microbiota in both the wild type and knockout mice was changed by antibiotics, but the recovery time was delayed in the knockouts compared to the wild type.

A similar result was observed in the newborns. After antibiotic treatment, which was completed at the time of weaning, the gut microbiota of both groups of mice was “significantly changed.” And, similar to adults, the knockout mice maintained reduced microbial diversity in the gut 14 days after the antibiotic treatment was stopped. In terms of the development of colitis, treatment did not affect the susceptibility of adults to colitis, but the neonatal knockout mice developed a more severe colitis. Interestingly, the researchers could transfer this severe colitis phenotype to other germ-free Nod2 knockout mice through the gut microbiota. They also found that this severe colitis phenotype was associated with changes in the intestinal T cells as well as the suite of cytokines found in the gut following inflammation, which taken together, indicates that Nod2  “has a critical role in shaping gut microbial responses and resilience to perturbations” and that the time of exposure is important.

It was known from previous work that while antibiotics do transiently change the gut microbiota of humans, the microbiota is usually fairly resilient and reverts back to its normal pre-treatment composition. According to the investigators, the fact that the Nod2 knockouts showed a delay in the time it took to revert back demonstrates reduced resilience of the gut microbiota, and this is the first study to show a role for Nod2 in microbial resilience following antibiotic exposure. The study also highlights the “long-lasting influence of an altered neonatal microbiota on mucosal immune homeostasis and development of disease.”


Goethel A, Turpin W, Rouquier S, et al. Nod2 influences microbial resilience and susceptibility to colitis following antibiotic exposure. Mucosal Immunol. 2019; 12: 720-732.