Qin JJ, Li RQ, Raes J, Arumugam M, Burgdorf KS, Manichanh C et al.. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-U70

BGI-Shenzhen, Shenzhen 518083, China.
Nature (Impact Factor: 41.46). 03/2010; 464(7285):59-65. DOI: 10.1038/nature08821
Source: PubMed


To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.

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    • "The advent of high-throughput sequencing technologies (Next-Generation Sequencing, commonly abbreviated to NGS) revolutionized this approach, by avoiding the need of cloning the DNA and thus greatly facilitating the obtention of metagenomic samples, at the same time drastically decreasing its price. Early examples of metagenomic projects include the analysis of samples of seawater [41] [15], human gut [36], or soil [43]. Present-day metagenomic studies focus on various bacterial, fungal or viral populations , exemplified by the Human Microbiome project [35] that investigates microbial communities at different sites of human body. "
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    • "For each sample, high quality reads were assembled to obtain long contigs by using SOAP denovo assembler (Li et al., 2010); the contigs longer than 500 bp were used to predict ORFs by MetaGene program (Noguchi, Park, & Takagi, 2006). Meanwhile , high quality reads from each sample were aligned against the Human Gut Gene Catalogue (Li et al., 2009; Qin et al., 2010) by SOAP2 (Li et al., 2009) using the criterion of identity ≥90%. We translated the aligned results to gene relative abundance by counting the number of reads that mapped to the gene. "
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