Genomic variation landscape of the human gut microbiome

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 () and Peer Bork ()
Additional contact information
Siegfried Schloissnig: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Manimozhiyan Arumugam: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Shinichi Sunagawa: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Makedonka Mitreva: The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Julien Tap: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Ana Zhu: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Alison Waller: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Daniel R. Mende: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Jens Roat Kultima: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
John Martin: The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Karthik Kota: The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Shamil R. Sunyaev: Brigham & Women’s Hospital & Harvard Medical School
George M. Weinstock: The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Peer Bork: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany

Nature, 2013, vol. 493, issue 7430, 45-50

Abstract: 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.

Date: 2013
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DOI: 10.1038/nature11711

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