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Genomic variation landscape of the human gut microbiome

机译：人类肠道微生物组的基因组变异景观

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摘要

欧洲MetaHIT项目和美国NIH Human Microbiome项目成员之间的一项合作，导致了一个rn用于“元基因组”变化分析的框架的建立，它rn被用来分析来自欧洲和北美洲的207个个体的rn252个粪便“元基因组”中的单核苷酸多态性、rn短插入／删除(indels)和结构变异体。变化模式rn表明，个体也许有独特的“元基因组”基因型，rn它们也许能提供与个性化的饮食或药物选择相rn关的数据。%Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake.
机译：欧洲MetaHIT项目和美国NIH Human Microbiome项目成员之间的一项合作，导致了一个rn用于“元基因组”变化分析的框架的建立，它rn被用来分析来自欧洲和北美洲的207个个体的rn252个粪便“元基因组”中的单核苷酸多态性、rn短插入／删除(indels)和结构变异体。变化模式rn表明，个体也许有独特的“元基因组”基因型，rn它们也许能提供与个性化的饮食或药物选择相rn关的数据。%Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake.

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  • 来源
    《Nature》 |2013年第7430期|45-50a3|共7页
  • 作者

    Siegfried Schloissnig; Manimozhiyan Arumugam; Shinichi Sunagawa; Makedonka Mitreva; Julien Tap; Ana Zhu; Alison Waller; Daniel R. Mende; Jens Roat Kultima; John Martin; Karthik Kota; Shamil R. Sunyaev; George M. Weinstock; Peer Bork;

  • 作者单位

    European Molecular Biology Laboratory, Meyerhofstrasse 1,69117 Heidelberg, Germany;

    European Molecular Biology Laboratory, Meyerhofstrasse 1,69117 Heidelberg, Germany;

    European Molecular Biology Laboratory, Meyerhofstrasse 1,69117 Heidelberg, Germany;

    The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA;

    European Molecular Biology Laboratory, Meyerhofstrasse 1,69117 Heidelberg, Germany;

    European Molecular Biology Laboratory, Meyerhofstrasse 1,69117 Heidelberg, Germany;

    European Molecular Biology Laboratory, Meyerhofstrasse 1,69117 Heidelberg, Germany;

    European Molecular Biology Laboratory, Meyerhofstrasse 1,69117 Heidelberg, Germany;

    European Molecular Biology Laboratory, Meyerhofstrasse 1,69117 Heidelberg, Germany;

    The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA;

    The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA;

    Division of Genetics, Department of Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, Massachusetts 02115, USA;

    The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA;

    European Molecular Biology Laboratory, Meyerhofstrasse 1,69117 Heidelberg, Germany,Max Delbruck Centre for Molecular Medicine, D-13092 Berlin, Germany;

  • 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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