Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut.
Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut.
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DOI：
10.1016/j.ymeth.2018.03.012
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发表时间：
2018-10-01
期刊：
影响因子：
--
通讯作者：
Chen Y
中科院分区：
文献类型：
--
作者：
Jameson E;Quareshy M;Chen Y
细菌途径以前已经阐明了三甲胺的形成。我们解释如何识别人类相关的细菌，产生三甲胺。如何识别哪些肠道细菌负责产生三甲胺。我们是否遗漏了什么-未知的细菌三甲胺形成途径？细菌形成的三甲胺（TMA）与心血管疾病有关。本文综述了用于研究人类肠道中由饮食胆碱和肉毒碱形成TMA的细菌的鉴定方法。最近的研究揭示了负责细菌TMA生产的代谢途径，主要是厌氧含甘氨酰自由基的胆碱-TMA裂解酶CutC和需氧肉毒碱单加氧酶CntA。这些酶的鉴定使得生物信息学方法能够筛选人类相关细菌分离物基因组和全肠道宏基因组，以确定哪些细菌负责人类肠道中的TMA形成。我们集中在几个关键的方法学方面，用于识别产TMA的细菌，并报告如何通过对现有细菌基因组和肠道宏基因组的生物信息学分析，在人类肠道微生物群中识别这些途径。
Bacterial pathways have previously been elucidated for trimethylamine formation. We explain how to identify human-associated bacteria that produce trimethylamine. How to identify which gut bacteria are responsible for producing trimethylamine. Are we missing anything – unknown bacterial trimethylamine formation pathways? The bacterial formation of trimethylamine (TMA) has been linked to cardiovascular disease. This review focuses on the methods employed to investigate the identity of the bacteria responsible for the formation of TMA from dietary choline and carnitine in the human gut. Recent studies have revealed the metabolic pathways responsible for bacterial TMA production, primarily the anaerobic glycyl radical-containing, choline-TMA lyase, CutC and the aerobic carnitine monooxygenase, CntA. Identification of these enzymes has enabled bioinformatics approaches to screen both human-associated bacterial isolate genomes and whole gut metagenomes to determine which bacteria are responsible for TMA formation in the human gut. We centre on several key methodological aspects for identifying the TMA-producing bacteria and report how these pathways can be identified in human gut microbiota through bioinformatics analysis of available bacterial genomes and gut metagenomes.
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影响因子：
3.7
作者：
Iwai S;Weinmaier T;Schmidt BL;Albertson DG;Poloso NJ;Dabbagh K;DeSantis TZ
通讯作者：
DeSantis TZ
影响因子：
8.6
作者：
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56.9
作者：
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通讯作者：
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影响因子：
3.5
作者：
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通讯作者：
Schmidt, Christian L.
DOI：
10.1073/pnas.1215689109
发表时间：
2012-12-26
影响因子：
11.1
作者：
Craciun, Smaranda;Balskus, Emily P.
通讯作者：
Balskus, Emily P.