Metagenomic Analysis of the Human Distal Gut Microbiome


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Metagenomic Analysis of the Human Distal Gut Microbiome

Steven R. Gill,1* Mihai Pop,1 Robert T. DeBoy,1 Paul B. Eckburg,2,3,4 Peter J. Turnbaugh,5 Buck S. Samuel,5 Jeffrey I. Gordon,5 David A. Relman,2,3,4 Claire M. Fraser-Liggett,1,6 Karen E. Nelson1


The human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed ~78 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. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-D-erythritol 4-phosphate pathway–mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.

1 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
2 Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
3 Department of Microbiology and Immunology, 299 Campus Drive, Stanford University, Stanford, CA 94305, USA.
4 Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
5 Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108, USA.
6 Departments of Pharmacology and Physiology and Microbiology and Tropical Diseases, George Washington University School of Medicine, Washington, DC 20037, USA.

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