Abstract A strategy to selectively target a microbial enzyme reduces the production of a metabolite linked to the development of cardiovascular disease.

The intestinal microbiome regulates host cellular functions linked to many human diseases. A new challenge is to translate preclinical microbiome studies into novel microbial therapies. In a new work, Roberts et al. build on research to therapeutically target trimethylamine N-oxide (TMAO), a microbiome-linked metabolite associated with platelet reactivity, atherosclerosis, and thrombosis.

TMAO is generated from microbial conversion of choline to trimethylamine (TMA) by the enzymes cutC and cutD (cutC/D), which is followed by oxidation in the liver. As choline is common in a Western diet, its metabolism by microbiota may link this diet to cardiovascular disease. The production of TMA from choline requires microbial metabolism: cutC/D cleaves a C–N bond that cannot be mediated by human enzymes. Using the cutC crystal structure, the authors predicted that cleavage of the iodinated choline analog iodomethylcholine (IMC) would generate a reactive by-product that inhibits cutC. The authors hypothesized that this therapy would selectively inhibit microbiome-mediated TMAO production without disrupting other human or microbiome functions. In vitro testing of IMC against a panel of commensal bacteria with cutC/D enzymes confirmed TMA inhibition without organism toxicity. In the same system, testing of other halogenated choline analogs identified fluoromethylcholine (FMC) as the most potent.

In mice, a single oral gavage of FMC inhibited >95% of plasma TMAO with no effect on blood choline concentration or choline-related metabolites, confirming microbial selectivity. FMC had no observed toxicity in mice or in human cell lines. In mouse models of thrombus formation and platelet aggregation, FMC was highly effective in reducing TMAO production and ameliorating phenotypes induced by a high-choline diet. Interestingly, despite FMC being nonlethal to microbes, there was a decrease in microbes associated with high-choline diets and a distinct ecology in FMC-treated mice relative to wild-type mice.

Researchers now have a novel strategy to target microbial biosynthetic pathways linked to cardiovascular disease in early-phase clinical trials. FMC highlights the highly touted safety profile that has driven an interest in microbial therapies but its unintended effect on microbial ecology demonstrates that “targeted” microbial manipulation may be a naïve goal in the microbiome, where species are deeply interconnected. Future human studies will be needed to confirm the safety of TMAO manipulation in humans and may need to consider how off-target microbial changes affect outcomes.