A human gut microbial gene catalogue established by metagenomic sequencing

Nature 464, 59-65 (4 March 2010) | doi:10.1038/nature08821; Received 14 August 2009; Accepted 23 December 2009

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, ~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.

It has been estimated that the microbes in our bodies collectively make up to 100 trillion cells, tenfold the number of human cells, and suggested that they encode 100-fold more unique genes than our own genome¹. The majority of microbes reside in the gut, have a profound influence on human physiology and nutrition, and are crucial for human life^{2, 3}. Furthermore, the gut microbes contribute to energy harvest from food, and changes of gut microbiome may be associated with bowel diseases or obesity^{4, 5, 6, 7, 8}.

To understand and exploit the impact of the gut microbes on human health and well-being it is necessary to decipher the content, diversity and functioning of the microbial gut community. 16S ribosomal RNA gene (rRNA) sequence-based methods⁹ revealed that two bacterial divisions, the Bacteroidetes and the Firmicutes, constitute over 90% of the known phylogenetic categories and dominate the distal gut microbiota¹⁰. Studies also showed substantial diversity of the gut microbiome between healthy individuals^{4, 8, 10, 11}. Although this difference is especially marked among infants¹², later in life the gut microbiome converges to more similar phyla.

Metagenomic sequencing represents a powerful alternative to rRNA sequencing for analysing complex microbial communities^{13, 14, 15}. Applied to the human gut, such studies have already generated some 3 gigabases (Gb) of microbial sequence from faecal samples of 33 individuals from the United States or Japan^{8, 16, 17}. To get a broader overview of the human gut microbial genes we used the Illumina Genome Analyser (GA) technology to carry out deep sequencing of total DNA from faecal samples of 124 European adults. We generated 576.7 Gb of sequence, almost 200 times more than in all previous studies, assembled it into contigs and predicted 3.3 million unique open reading frames (ORFs). This gene catalogue contains virtually all of the prevalent gut microbial genes in our cohort, provides a broad view of the functions important for bacterial life in the gut and indicates that many bacterial species are shared by different individuals. Our results also show that short-read metagenomic sequencing can be used for global characterization of the genetic potential of ecologically complex environments.