DOI: 10.1126/science.1124234 , 1355 (2006); 312Science et al.Steven R. Gill,MicrobiomeMetagenomic Analysis of the Human Distal Gut www.sciencemag.org (this information is current as of August 14, 2009 ):The following resources related to this article are available online at http://www.sciencemag.org/cgi/content/full/312/5778/1355version of this article at: including high-resolution figures, can be found in the onlineUpdated information and services, http://www.sciencemag.org/cgi/content/full/312/5778/1355/DC1 can be found at: Supporting Online Materialfound at: can berelated to this articleA list of selected additional articles on the Science Web sites http://www.sciencemag.org/cgi/content/full/312/5778/1355#otherarticles, 16 of which can be accessed for free: cites 29 articlesThis article 300 article(s) on the ISI Web of Science. cited byThis article has been http://www.sciencemag.org/cgi/content/full/312/5778/1355#otherarticles 76 articles hosted by HighWire Press; see: cited byThis article has been http://www.sciencemag.org/cgi/collection/geneticsGenetics : subject collectionsThis article appears in the following http://www.sciencemag.org/about/permissions.dtl in whole or in part can be found at: this articlepermission to reproduce of this article or about obtaining reprintsInformation about obtaining registered trademark of AAAS. is aScience2006 by the American Association for the Advancement of Science; all rights reserved. The title CopyrightAmerican Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by theScience on August 14, 2009 www.sciencemag.orgDownloaded fromMetagenomic Analysis of the HumanDistal Gut MicrobiomeSteven R. Gill,1*‡ Mihai Pop,1† Robert T. DeBoy,1Paul B. Eckburg,2,3,4Peter J. Turnbaugh,5Buck S. Samuel,5Jeffrey I. Gordon,5David A. Relman,2,3,4Claire M. Fraser-Liggett,1,6Karen E. Nelson1The human intestinal microbiota is composed of 1013to 1014microorganisms whose collectivegenome (‘‘microbiome’’) contains at least 100 times as many genes as our own genome. Weanalyzed È78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction–amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Usingmetabolic function analyses of identified genes, we compared our human genome with the averagecontent of previously sequenced microbial genomes. Our microbiome has significantly enrichedmetabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-D-erythritol 4-phosphate pathway–mediated biosynthesis of vitamins and isoprenoids. Thus, humans aresuperorganisms whose metabolism represents an amalgamation of microbial and human attributes.Our body surfaces are home to micro-bial communities whose aggregatemembership outnumbers our humansomatic and germ cells by at least an order ofmagnitude. The vast majority of these microbes(10 to 100 trillion) inhabit our gastrointestinaltract, with the greatest number residing in thedistal gut, where they synthesize essentialamino acids and vitamins and process compo-nents of otherwise indigestible contributions toour diet such as plant polysaccharides (1). Themost comprehensive 16S ribosomal DNA(rDNA) sequence-based enumeration of thedistal gut and fecal microbiota published to dateunderscores its highly selected nature. Amongthe 70 divisions (deep evolutionary lineages) ofBacteria and 13 divisions of Archaea describedto date, the distal gut and fecal microbiota of thethree healthy adults surveyed was dominated byjust two bacterial divisions, the Bacteroidetesand the Firmicutes, which made up 999% of theidentified phylogenetic types (phylotypes), andby one prominent methanogenic archaeon,Methanobrevibacter smithii (2). The humandistal gut microbiome is estimated to containQ100 times as many genes as our 2.85–billionbase pair (bp) human genome (1). Therefore, asuperorganismal view of our genetic landscapeshould include genes embedded in our humangenome and the genes in our affiliated micro-biome, whereas a comprehensive view of ourmetabolome would encompass the metabolicnetworks based in our microbial communities.Progress made with 16S rDNA-based enu-merations has disclosed significant differencesin community membership between healthyadults (2, 3), differences that may contribute tovariations in normal physiology between individ-uals or that may predispose to disease. For ex-ample, studies of humans and gnotobiotic mousemodels indicate that our mutualistic relations withthe gut microbiota influence maturation of theimmune system (4), modulate responses to epi-thelial cell injury (5) , affect energy balance (6),and support biotransformations that we are ill-equipped to perform on our own, including pro-cessing of xenobiotics (7). However, we arelimited by our continued inability to cultivate themajority of our indigenous microbial communitymembers, biases introduced by preferential poly-merase chain reaction (PCR) amplification of 16SrDNA genes and by our limited ability to inferorganismal function from these gene sequences.As with soil (8) and ocean (9), metagenomicanalysis of complex communiti es offers an op-portunity to examine in a comprehensive mannerhow ecosystems respond to environmental per-turbations, and in the case of humans, how ourmicrobial ecosystems contribute to health anddisease. In the current study, we use a metage-nomics approach to reveal microbial genomicand genetic diversity and to identify some of thedistinctive functional attributes encoded in ourdistal gut microbiome.Sequencing the microbiome. Althoughwh o le - genome shotgun sequencing and assem-bly have historically been applied to the studyof single organisms, recent reports from Venteret al.(9) and Baker et al.(10) have demon-strated the utility of this approach for studyingmixed microbial communities. Variations in therelative abundance of each member of the mi-crobial community and their respective genomesizes d etermine the final depth of sequencecoverage for any organism at a particular levelof sequencing. This means that the genome se-quences of abundant species will be well rep-resented in a set of random shotgun reads,whereas lower abundance species may be rep-resented by a small number of sequences. Infact, the size and depth of coverage (computedas the ratio between the total length of the readsplaced into
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