DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome
DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome
复制标题
DNA 硫代磷酸酯修饰广泛分布于人类微生物组中
DOI：
10.3390/biom10081175
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发表时间：
2020-08-01
期刊：
影响因子：
5.5
通讯作者：
You, Delin
中科院分区：
文献类型：
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作者：
Sun, Yihua;Kong, Lingxin;You, Delin
存在于许多原核生物中的DNA硫代磷酸酯（PT）修饰，包括细菌病原体和细菌，赋予多种特征，包括限制基因转移，影响全局转录反应，以及在暴露于炎症化学介质期间降低适应性。虽然含PT的细菌已在各种环境中进行了研究，但尚未在人体微生物组中进行研究。在这里，我们调查了携带PT的菌株的分布，并验证了它们在人类微生物组中的存在。我们发现超过2000株含PT基因的菌株分布在不同的身体部位，特别是在胃肠道。PT修饰基因优先分布在几个属中，包括假单胞菌属、梭菌属和埃希氏菌属，具有遗传多样性。我们还评估了PT修饰模式，并在人粪便DNA中发现了六个新的PT连接的二核苷酸（CpsG，CpsT，ApsG，TpsG，GpsC，ApsT）。为了进一步研究人类肠道微生物组中的PT，我们分析了PT修饰基因的丰度并定量了粪便DNA中的PT连接的二核苷酸。这些结果证实，人类微生物组是含PT微生物的丰富储存库，并且包含多种PT修饰模式。
The DNA phosphorothioate (PT) modification existing in many prokaryotes, including bacterial pathogens and commensals, confers multiple characteristics, including restricting gene transfer, influencing the global transcriptional response, and reducing fitness during exposure to chemical mediators of inflammation. While PT-containing bacteria have been investigated in a variety of environments, they have not been studied in the human microbiome. Here, we investigated the distribution of PT-harboring strains and verified their existence in the human microbiome. We found over 2000 PT gene-containing strains distributed in different body sites, especially in the gastrointestinal tract. PT-modifying genes are preferentially distributed within several genera, including Pseudomonas, Clostridioides, and Escherichia, with phylogenic diversities. We also assessed the PT modification patterns and found six new PT-linked dinucleotides (CpsG, CpsT, ApsG, TpsG, GpsC, ApsT) in human fecal DNA. To further investigate the PT in the human gut microbiome, we analyzed the abundance of PT-modifying genes and quantified the PT-linked dinucleotides in the fecal DNA. These results confirmed that human microbiome is a rich reservoir for PT-containing microbes and contains a wide variety of PT modification patterns.