The microbiome of NLR knockout animals reveals insights into susceptibility to experimental colitis.

Abstract

Abstract Upon sensing particular pathogen associated molecular patterns (PAMPs), inflammasome-forming NOD-like receptors (NLRs) initiate pyroptosis and the cleavage of pro IL-18 and pro IL-1β to their active forms. Consequently, the absence of an NLR or its malfunction in the gut has been shown to result in dysbiosis. There is significant evidence linking dysbiosis with chronic inflammation in the gut and colon cancer. Prior work in our laboratory has revealed that mice lacking NLR inflammasomes, specifically Nlrp1−/− mice, are highly susceptible to experimental colitis and colitis-associated cancer. Here, we extend these findings by evaluating the microbiome of mice lacking either Asc or Nlrp1. 16s rRNA sequencing revealed 6 unique genera prevalent in Nlrp1−/− mice compared to WT and 9 genera in Asc−/− mice compared to WT. Remarkably, the microbiome composition in both knockout animals was more pathogenic, including such genera as Helicobacter, Mucispirillum, and Clostridium. The abundance of volatile free fatty acids was assessed to investigate functional metabolic differences due to the uniqueness of the microbiome in these animals, and interestingly the abundance of acetate, butyrate, and proprionate were distinctly different in Nlrp1−/− and Asc−/− mice compared to WT. Crucially, our analyses were conducted prior to any experimental colitis model. The differences in the microbiomes of these mice have the potential to resolve conflicting data in the field regarding inflammasome deficient mice and subsequent predisposition to or protection from colitis and cancer. Future work will establish which NLR is responsible for sensing the specific bacteria present in the microbiome of the inflammasome-deficient mice at rest.