Uncovering the trimethylamine-producing bacteria of the human gut microbiota.
Uncovering the trimethylamine-producing bacteria of the human gut microbiota.
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DOI：
10.1186/s40168-017-0271-9
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发表时间：
2017-05-15
期刊：
影响因子：
15.5
通讯作者：
Vital M
中科院分区：
文献类型：
--
作者：
Rath S;Heidrich B;Pieper DH;Vital M
三甲胺（TMA）由肠道微生物群从膳食季胺（主要是胆碱和肉碱）中产生，与动脉粥样硬化和严重心血管疾病有关。目前，关于肠道中TMA产生物的组成信息很少，因为它们的丰度很低，而且由于许多分类群显示出不同的产生该化合物的能力，需要基于特定功能的检测方法。为了研究微生物群落形成tma的潜力，我们建立了主要tma合成途径的关键基因数据库，编码胆碱tma裂解酶（cutC）和肉碱加氧酶（cntA），采用多级别筛选方法，在67134个基因组中分别发现了1107个和6738个候选基因，分别表现出cutC和cntA。通过定量PCR列举TMA产生菌群，并通过Illumina测序表征其组成，开发了基因靶向测定方法，并应用于人类粪便样本（n = 50），其中所有样本都含有潜在的TMA产生菌（在所有个体中检测到cutC，而只有26%含有cntA），但仅占总群落的一小部分（在大多数样本中低于1%）。获得的cutC扩增子与各种分类群相关，特别是与Clostridium XIVa菌株和Eubacterium sp.菌株AB3007菌株相关，尽管大部分序列与参考文献的核苷酸同源性较低（平均86%±7%），表明关键的人类TMA产生物尚未分离。共现分析揭示了不同样品中特定的类群支配着cut - c表现类群的群落结构。CntA扩增子对主要来自大肠杆菌的γ变形菌具有很高的特异性（~99%）。由人类微生物组计划提供的样本（n = 154）的宏基因组分析证实了丰度模式以及通过我们的分析获得的总体分类组成，尽管分辨率要低得多，而16S核糖体RNA基因序列分析不能充分揭示tma产生的潜力。在这项研究中，我们开发了一种诊断框架，可以量化和全面表征人类粪便样本中tma产生潜力。我们确定了关键的参与者，并利用功能基因组学对最密切相关的参考菌株进行了环境生态位预测，为制定抑制TMA生产者和限制其增殖的特定治疗策略提供了重要信息。本文的在线版本（doi:10.1186/s40168-017-0271-9）包含补充材料，可供授权用户使用。
Trimethylamine (TMA), produced by the gut microbiota from dietary quaternary amines (mainly choline and carnitine), is associated with atherosclerosis and severe cardiovascular disease. Currently, little information on the composition of TMA producers in the gut is available due to their low abundance and the requirement of specific functional-based detection methods as many taxa show disparate abilities to produce that compound. In order to examine the TMA-forming potential of microbial communities, we established databases for the key genes of the main TMA-synthesis pathways, encoding choline TMA-lyase (cutC) and carnitine oxygenase (cntA), using a multi-level screening approach on 67,134 genomes revealing 1107 and 6738 candidates to exhibit cutC and cntA, respectively. Gene-targeted assays enumerating the TMA-producing community by quantitative PCR and characterizing its composition via Illumina sequencing were developed and applied on human fecal samples (n = 50) where all samples contained potential TMA producers (cutC was detected in all individuals, whereas only 26% harbored cntA) constituting, however, only a minor part of the total community (below 1% in most samples). Obtained cutC amplicons were associated with various taxa, in particular with Clostridium XIVa strains and Eubacterium sp. strain AB3007, though a bulk of sequences displayed low nucleotide identities to references (average 86% ± 7%) indicating that key human TMA producers are yet to be isolated. Co-occurrence analysis revealed specific groups governing the community structure of cutC-exhibiting taxa across samples. CntA amplicons displayed high identities (~99%) to Gammaproteobacteria-derived references, primarily from Escherichia coli. Metagenomic analysis of samples provided by the Human Microbiome Project (n = 154) confirmed the abundance patterns as well as overall taxonomic compositions obtained with our assays, though at much lower resolution, whereas 16S ribosomal RNA gene sequence analysis could not adequately uncover the TMA-producing potential. In this study, we developed a diagnostic framework that enabled the quantification and comprehensive characterization of the TMA-producing potential in human fecal samples. The key players were identified, and together with predictions on their environmental niches using functional genomics on most closely related reference strains, we provide crucial information for the development of specific treatment strategies to restrain TMA producers and limit their proliferation. The online version of this article (doi:10.1186/s40168-017-0271-9) contains supplementary material, which is available to authorized users.