Metagenomic Analysis Of The Human Distal Gut Microbiome

RESEARCH ARTICLE 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 atleast 100 times as many genes as our own genome. We analyzed 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. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiomehas significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-D-erythritol 4phosphate pathway–mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes. ur body surfaces are home to microbial communities whose aggregate membership outnumbers ourhuman somatic and germ cells by at least an order of magnitude. The vast majority of these microbes (10 to 100 trillion) inhabit our gastrointestinal tract, with the greatest number residing in the distal gut, where they synthesize essential amino acids and vitamins and process components of otherwise indigestible contributions to our diet such as plant polysaccharides (1). The most comprehensive 16Sribosomal DNA (rDNA) sequence-based enumeration of the distal gut and fecal microbiota published to date underscores its highly selected nature. Among the 70 divisions (deep evolutionary lineages) of Bacteria and 13 divisions of Archaea described to date, the distal gut and fecal microbiota of the three healthy adults surveyed was dominated by just two bacterial divisions, the Bacteroidetes andthe Firmicutes, which made up 999% of the identified phylogenetic types (phylotypes), and by one prominent methanogenic archaeon, Methanobrevibacter smithii (2). The human distal gut microbiome is estimated to contain of single organisms, recent reports from Venter et al. (9) and Baker et al. (10) have demonstrated the utility of this approach for studying mixed microbial communities. Variations inthe relative abundance of each member of the microbial community and their respective genome sizes determine the final depth of sequence coverage for any organism at a particular level of sequencing. This means that the genome sequences of abundant species will be well represented in a set of random shotgun reads, whereas lower abundance species may be represented by a small number of sequences.In fact, the size and depth of coverage (computed as the ratio between the total length of the reads placed into contigs and the total size of the contigs) of genome assemblies generated from a metagenomics project can provide information on relative species abundance. A total of 65,059 and 74,462 high-quality sequence reads were generated from random DNA libraries created with fecal specimens oftwo healthy humans (subjects 7 and 8). These two subjects, ages 28 and 37, female and male, respectively, had not used antibiotics or any other medications during the year before specimen collection (11). The combined sequenced distal gut ‘‘microbiome’’ of subjects 7 and 8 consisted of 17,668 contigs that assembled into 14,572 scaffolds, totaling 33,753,108 bp. The scaffolds ranged in size from1000 to 57,894 bp and the contigs from 92 to 44,747 bp. The average depth of sequence coverage in contigs was 2.13-fold. Forty percent of the reads (56,292 total) could not be assembled into contigs, most likely because of a combination of low depth of coverage and low abundance of some organisms within the specimens. Together, these singletons accounted for an additional 45,078,063 bp of DNA. A...