ABSTRACT: BACKGROUND:l-Carnitine, an abundant nutrient in red meat, accelerates atherosclerosis in mice via gut microbiota-dependent formation of trimethylamine (TMA) and trimethylamine N-oxide (TMAO) via a multistep pathway involving an atherogenic intermediate, ?-butyrobetaine (?BB). The contribution of ?BB in gut microbiota-dependent l-carnitine metabolism in humans is unknown. METHODS:Omnivores and vegans/vegetarians ingested deuterium-labeled l-carnitine (d3-l-carnitine) or ?BB (d9-?BB), and both plasma metabolites and fecal polymicrobial transformations were examined at baseline, following oral antibiotics, or following chronic (?2 months) l-carnitine supplementation. Human fecal commensals capable of performing each step of the l-carnitine??BB?TMA transformation were identified. RESULTS:Studies with oral d3-l-carnitine or d9-?BB before versus after antibiotic exposure revealed gut microbiota contribution to the initial 2 steps in a metaorganismal l-carnitine??BB?TMA?TMAO pathway in subjects. Moreover, a striking increase in d3-TMAO generation was observed in omnivores over vegans/vegetarians (>20-fold; P = 0.001) following oral d3-l-carnitine ingestion, whereas fasting endogenous plasma l-carnitine and ?BB levels were similar in vegans/vegetarians (n = 32) versus omnivores (n = 40). Fecal metabolic transformation studies, and oral isotope tracer studies before versus after chronic l-carnitine supplementation, revealed that omnivores and vegans/vegetarians alike rapidly converted carnitine to ?BB, whereas the second gut microbial transformation, ?BB?TMA, was diet inducible (l-carnitine, omnivorous). Extensive anaerobic subculturing of human feces identified no single commensal capable of l-carnitine?TMA transformation, multiple community members that converted l-carnitine to ?BB, and only 1 Clostridiales bacterium, Emergencia timonensis, that converted ?BB to TMA. In coculture, E. timonensis promoted the complete l-carnitine?TMA transformation. CONCLUSION:In humans, dietary l-carnitine is converted into the atherosclerosis- and thrombosis-promoting metabolite TMAO via 2 sequential gut microbiota-dependent transformations: (a) initial rapid generation of the atherogenic intermediate ?BB, followed by (b) transformation into TMA via low-abundance microbiota in omnivores, and to a markedly lower extent, in vegans/vegetarians. Gut microbiota ?BB?TMA/TMAO transformation is induced by omnivorous dietary patterns and chronic l-carnitine exposure. TRIAL REGISTRATION:ClinicalTrials.gov NCT01731236. FUNDING:NIH and Office of Dietary Supplements grants HL103866, HL126827, and DK106000, and the Leducq Foundation.