An integrated metagenomics and metabolomics approach implicates the microbiome-gut-brain-axis in the pathogenesis of Huntington’s disease transgenic mice

Abstract Background: Huntington’s disease (HD) is an autosomal dominant neurodegenerative disorder with onset and severity of symptoms influenced by various environmental factors. Recent discoveries have highlighted the importance of the gastrointestinal microbiome in mediating the bidirectional communication between the central and enteric nervous system via circulating factors. Using shotgun sequencing, we investigated the gut microbiome composition in the R6/1 transgenic mouse model of HD from 4 to 12 weeks of age (early adolescent through to adult stages). Targeted metabolomics was also performed on the blood plasma of these mice (n=9 per group) at 12 weeks of age to investigate potential effects of gut dysbiosis on the plasma metabolome profile. The short-chain fatty acid (SCFA) concentrations in the plasma were validated using LCMS. Results: Beta diversity differed between HD mice compared to their WT littermates at 12 weeks of age, suggesting that gut dysbiosis occurs prior to overt motor symptoms. Modelled time profiles of each species, KEGG Orthologs and bacterial genes, revealed heightened volatility in the HD mice, indicating potential early effects of HD mutation in the gut prior to significant cognitive and motor dysfunction. In addition to gut dysbiosis at 12 weeks of age, we also found functional differences between the WT and HD mice. The butanoate metabolism pathway, which leads to the production of the protective short-chain fatty acid, butyrate, was increased in the gut. However, the plasma concentration of butyrate and propionate were both decreased in the HD mice, as determined by the SCFA validation. The concentrations of ATP were increased by over 4-fold in the HD plasma, which was contrary to expectations. The statistical integration of the metagenomics and metabolomics unraveled several Bacteroides species that were positively correlated with butyrate levels, and negatively correlated with ATP and pipecolic acid in the plasma. Blautia producta and Prevotella scopos were found to be negatively correlated with the butyrate and ATP respectively. Conclusions: Our study has revealed a previously unknown relationship between the gut bacteria and plasma metabolome, suggesting the potential role of gut in modulating the pathogenesis of HD via specific altered plasma metabolites which mediate gut-brain signalling.