TY - JOUR
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
N1 - Funding Information:
Acknowledgements The authors are grateful to J. Korbel and the members of the Bork group atEMBLfor discussions andassistance, especiallyS.Powellfor performingsome of the computations. We thank the EMBL IT core facility and Y. Yuan for managing the high-performance computing resources. We would like to thank J. I. Gordon for providing three of the samples used. We are also grateful to the European MetaHIT consortium and the NIH Common Fund Human Microbiome Project Consortium for generating and making available the data sets used in this study. The research leading to these results has received funding from EMBL, the European Community’s Seventh Framework Programme via the MetaHIT (HEALTH-F4-2007-201052) and IHMS (HEALTH-F4-2010-261376) grants as well as from the National Institutes of Health grants U54HG003079 and U54HG004968.
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.
UR - http://www.scopus.com/inward/record.url?scp=84871732071&partnerID=8YFLogxK
U2 - 10.1038/nature11711
DO - 10.1038/nature11711
M3 - Article
C2 - 23222524
AN - SCOPUS:84871732071
SN - 0028-0836
VL - 493
SP - 45
EP - 50
JO - Nature
JF - Nature
IS - 7430
ER -