Genomic variation landscape of the human gut microbiome View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-12-05

AUTHORS

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

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. More... »

PAGES

45-50

Journal

TITLE

Nature

ISSUE

7430

VOLUME

493

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nature11711

DOI

http://dx.doi.org/10.1038/nature11711

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1004024856

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/23222524


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46 deletion
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75 nucleotide polymorphisms
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