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Ecology drives a global network of gene exchange connecting the human microbiome

机译：生态驱动连接人类微生物组的全球基因交换网络

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Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence, antibiotic resistance and xenobiotic metabolism to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events. Here we report the discovery and characterization of a vast, human-associated network of gene exchange, large enough to directly compare the principal forces shaping HGT. We show that this network of 10,770 unique, recently transferred (more than 99% nudeotide identity) genes found in 2,235 full bacterial genomes, is shaped principally by ecology rather than geography or phylogeny, with most gene exchange occurring between isolates from ecologically similar, but geographically separated, environments. For example, we observe 25-fold more HGT between human-associated bacteria than among ecologically diverse non-human isolates (P= 3.0 X 10~(270)). Weshowthat within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.
机译：从非亲代谱系获得遗传物质的水平基因转移（HGT）在细菌进化中很重要。尤其是，HGT提供了快速获取基因创新的途径，从而使诸如毒力，抗生素抗性和异种生物新陈代谢等特征通过人类微生物组传播。最近的轶事研究提供了活跃的基因在人体上流动的快照，强调了确定这种近期转移的频率以及控制这些事件的力量的必要性。在这里，我们报道了一个庞大的，与人类相关的基因交换网络的发现和表征，该网络足够大，可以直接比较影响HGT的主要力量。我们显示，在2235个完整细菌基因组中发现的10,770个独特的，最近已转移的（超过99％的核苷酸相似性）基因网络，主要是由生态学而非地理或系统发育塑造而成，大多数基因交换发生在生态相似的菌株之间地理位置分离的环境。例如，我们观察到人类相关细菌之间的HGT比生态上多样化的非人类分离株高25倍（P = 3.0 X 10〜（270））。我们表明，在人类微生物组中，这种生态体系结构在多个空间尺度，功能类别和生态位中继续存在，并且转移在居住于同一身体部位，具有相同耐氧性或具有相同致病能力的细菌之间进一步丰富。这种结构为定义生态位的分子特性提供了一个窗口，我们可以利用这些见解来发现抗生素抗药性的来源，并鉴定与脑膜炎和其他疾病的病理学相关的基因。

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  • 来源
    《Nature》 |2011年第7376期|p.241-244|共4页
  • 作者

    Chris S. Smillie; Mark B. Smith; Jonathan Friedman; Otto X. Cordero; Lawrence A. David; Eric J. Aim;

  • 作者单位

    Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;

    Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;

    Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;

    Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;

    Society of Fellows, Harvard University, Cambridge, Massachusetts 02138, USA;

    Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA,Broad Institute, Cambridge, Massachusetts 02139, USA;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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