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; Peer Bork

doi:10.1038/nature11711

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, Peer Bork

441 Citations (Scopus)

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.

Original language	English
Journal	Nature
Volume	493
Issue number	7430
Pages (from-to)	45-50
Number of pages	6
DOIs	https://doi.org/10.1038/nature11711
Publication status	Published - 3 Jan 2013

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title = "Genomic variation landscape of the human gut microbiome",

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.",

author = "Siegfried Schloissnig and Manimozhiyan Arumugam and Shinichi Sunagawa and Makedonka Mitreva and Julien Tap and Ana Zhu and Alison Waller and Mende, {Daniel R} and Kultima, {Jens Roat} and John Martin and Karthik Kota and Sunyaev, {Shamil R} and Weinstock, {George M} and Peer Bork",

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T1 - Genomic variation landscape of the human gut microbiome

AU - Schloissnig, Siegfried

AU - Arumugam, Manimozhiyan

AU - Sunagawa, Shinichi

AU - Mitreva, Makedonka

AU - Tap, Julien

AU - Zhu, Ana

AU - Waller, Alison

AU - Mende, Daniel R

AU - Kultima, Jens Roat

AU - Martin, John

AU - Kota, Karthik

AU - Sunyaev, Shamil R

AU - Weinstock, George M

AU - Bork, Peer

PY - 2013/1/3

Y1 - 2013/1/3

N2 - 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.

AB - 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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Genomic variation landscape of the human gut microbiome

Abstract

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