Several lines of evidence including detection of bacterial DNA in atherosclerotic plaques and the impact of bacterial metabolites on cardiovascular disease implicate an emerging role of microorganisms in cardiovascular health. Here, we investigate whether the gut microbiome is associated with carotid ultrasound measurements, a diagnostic measure for carotid artery disease and risk of stroke, in an average risk asymptomatic population based cohort. We identified for the first time E. coli and K. pneumoniae to be consistently associated with undesirable carotid ultrasound and lipid parameters in otherwise asymptomatic average-risk individuals. These data highlight a need to understand their potential role as biomarkers and how they may be involved in future risk of cardiovascular diseases.