Trimethylamine (TMA) is an important gut microbial metabolite strongly associated with human disease. There are prominent gaps in our understanding of how TMA is produced from the essential dietary nutrient L-carnitine, particularly in the anoxic environment of the human gut where oxygen-dependent L-carnitine-metabolizing enzymes are likely inactive. Here, we elucidate the chemical and genetic basis for anaerobic TMA generation from the L-carnitine-derived metabolite γ-butyrobetaine (γbb) by the human gut bacterium Emergencia timonensis. We identify a set of genes upregulated by γbb and demonstrate that the enzymes encoded by the induced γbb utilization (bbu) gene cluster convert γbb to TMA. The key TMA-generating step is catalyzed by a previously unknown type of TMA-lyase enzyme that utilizes a flavin cofactor to catalyze a redox neutral transformation. We identify additional cultured and uncultured host-associated bacteria that possess the bbu gene cluster, providing insights into the distribution of anaerobic γbb metabolism. Lastly, we present genetic, transcriptional, and metabolomic evidence that confirms the relevance of this metabolic pathway in the human gut microbiota. These analyses indicate that the anaerobic pathway is a more substantial contributor to TMA generation from L-carnitine in the human gut than the previously proposed aerobic pathway. The discovery and characterization of the bbu pathway provides the critical missing link in anaerobic metabolism of L-carnitine to TMA, enabling investigation into the connection between this microbial function and human disease.

中文翻译：

---

阐明人肠细菌中L-肉碱衍生的γ-丁甜菜碱代谢为三甲胺的厌氧途径

三甲胺（TMA）是与人类疾病密切相关的重要肠道微生物代谢产物。在我们对必需的饮食营养素左旋肉碱如何产生TMA的理解上存在明显的差距，特别是在人体肠道的缺氧环境中，其中依赖氧的左旋肉碱代谢酶可能没有活性。在这里，我们阐明了人类肠道细菌Emergencia timonensis从L-肉碱衍生的代谢物γ-butyrobetaine（γbb）产生厌氧TMA的化学和遗传基础。我们确定了一组由γbb上调的基因，并证明了由诱导的γbb利用（bbu）基因簇编码的酶将γbb转换为TMA。关键的TMA产生步骤是由以前未知类型的TMA裂解酶催化的，该酶利用黄素辅因子催化氧化还原中性转化。我们确定了具有bbu基因簇的其他培养的和未培养的宿主相关细菌，提供了厌氧性γbb代谢分布的见解。最后，我们提出了遗传，转录和代谢组学证据，证实了该代谢途径在人体肠道菌群中的相关性。这些分析表明，与先前提出的有氧途径相比，厌氧途径对人肠道中左旋肉碱产生TMA的贡献更大。bbu途径的发现和表征为L-肉碱到TMA的厌氧代谢提供了关键的缺失环节，