The relationship between gut microbiota composition and the development of cardiovascular disease, with a potential role of microbial metabolites in inflammatory and metabolic pathways is of interest. We analyzed gut microbiota and markers of cardiovascular health in a cohort of 100 participants for three years to search for microbial signatures correlated with increased CVD risk. Our results show several correlations between specific microbial taxa, lipid metabolism and systemic inflammation, whereby a higher Firmicutes/Bacteroides ratio is associated with a greater incidence of CVD. These results suggest that intervention targeting the microbiome has the potential to reduce risk for CVD and point towards a role for gut microbiota in cardiovascular health.