Genomic variation landscape of the human gut microbiome
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 met...
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| Published in | Nature (London) Vol. 493; no. 7430; pp. 45 - 50 |
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| Main Authors | , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
03.01.2013
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | 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.
A framework for metagenomic variation analysis to explore variation in the human microbiome is developed; the study describes SNPs, short indels and structural variants in 252 faecal metagenomes of 207 individuals from Europe and North America.
Gene variation in human gut microbes
A collaboration between members of the European MetaHIT and American NIH Human Microbiome projects has led to the development of a framework for metagenomic variation analysis, which is used to analyse single nucleotide polymorphisms, short indels and structural variants in 252 faecal metagenomes of 207 individuals from Europe and North America. Variation patterns suggest that individuals might have unique metagenomic genotypes that could provide data relevant to personalized dietary or drug choices. |
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| AbstractList | 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.
A framework for metagenomic variation analysis to explore variation in the human microbiome is developed; the study describes SNPs, short indels and structural variants in 252 faecal metagenomes of 207 individuals from Europe and North America.
Gene variation in human gut microbes
A collaboration between members of the European MetaHIT and American NIH Human Microbiome projects has led to the development of a framework for metagenomic variation analysis, which is used to analyse single nucleotide polymorphisms, short indels and structural variants in 252 faecal metagenomes of 207 individuals from Europe and North America. Variation patterns suggest that individuals might have unique metagenomic genotypes that could provide data relevant to personalized dietary or drug choices. 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. 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 thehuman microbiome.Wetherefore 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 ofSNPvariation 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. [PUBLICATION ABSTRACT] While large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the latter is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 fecal 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 indels, 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 implies 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. 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.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. |
| Audience | Academic |
| Author | Bork, Peer Kultima, Jens Roat Mende, Daniel R. Martin, John Schloissnig, Siegfried Zhu, Ana Kota, Karthik Waller, Alison Weinstock, George M. Sunyaev, Shamil R. Arumugam, Manimozhiyan Mitreva, Makedonka Tap, Julien Sunagawa, Shinichi |
| AuthorAffiliation | 1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany 4 Max Delbrück Centre for Molecular Medicine, D-13092 Berlin, Germany 3 Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA 2 The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St. Louis, MO 63108, USA |
| AuthorAffiliation_xml | – name: 3 Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA – name: 4 Max Delbrück Centre for Molecular Medicine, D-13092 Berlin, Germany – name: 2 The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St. Louis, MO 63108, USA – name: 1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany |
| Author_xml | – sequence: 1 givenname: Siegfried surname: Schloissnig fullname: Schloissnig, Siegfried organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany – sequence: 2 givenname: Manimozhiyan surname: Arumugam fullname: Arumugam, Manimozhiyan organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany – sequence: 3 givenname: Shinichi surname: Sunagawa fullname: Sunagawa, Shinichi organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany – sequence: 4 givenname: Makedonka surname: Mitreva fullname: Mitreva, Makedonka organization: The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA – sequence: 5 givenname: Julien surname: Tap fullname: Tap, Julien organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany – sequence: 6 givenname: Ana surname: Zhu fullname: Zhu, Ana organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany – sequence: 7 givenname: Alison surname: Waller fullname: Waller, Alison organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany – sequence: 8 givenname: Daniel R. surname: Mende fullname: Mende, Daniel R. organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany – sequence: 9 givenname: Jens Roat surname: Kultima fullname: Kultima, Jens Roat organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany – sequence: 10 givenname: John surname: Martin fullname: Martin, John organization: The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA – sequence: 11 givenname: Karthik surname: Kota fullname: Kota, Karthik organization: The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA – sequence: 12 givenname: Shamil R. surname: Sunyaev fullname: Sunyaev, Shamil R. organization: Division of Genetics, Department of Medicine, Brigham & Women’s Hospital & Harvard Medical School – sequence: 13 givenname: George M. surname: Weinstock fullname: Weinstock, George M. email: gweinsto@genome.wustl.edu organization: The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA – sequence: 14 givenname: Peer surname: Bork fullname: Bork, Peer email: bork@embl.de organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany , Max Delbrück Centre for Molecular Medicine |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=26756583$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/23222524$$D View this record in MEDLINE/PubMed |
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| CODEN | NATUAS |
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| ContentType | Journal Article |
| Copyright | Springer Nature Limited 2012 2014 INIST-CNRS COPYRIGHT 2013 Nature Publishing Group Copyright Nature Publishing Group Jan 3, 2013 |
| Copyright_xml | – notice: Springer Nature Limited 2012 – notice: 2014 INIST-CNRS – notice: COPYRIGHT 2013 Nature Publishing Group – notice: Copyright Nature Publishing Group Jan 3, 2013 |
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| Title | Genomic variation landscape of the human gut microbiome |
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