A human gut microbial gene catalog established by metagenomic sequencing

By J. Qin, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, K. Burgdorf, C. Manichanh, T. Nielsen, N. Pons, F. Levenez, Takuji Yamada and 43 more. Nature, 2010

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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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cef14e7cd0eac6cbda2b9960b1e4c91acf8d028b

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Citations in the corpus

From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome (2012, background): “The bacterial contribution to the total genetic diversity found within the human body is perhaps a more important consideration as the number of bacterial genes clearly outnumbers the number of genes in the human genome by several orders of magnitude (Qin et al. 2010).”
Clustering metagenomic sequences with interpolated Markov models (2010, background): “Successful metagenomics projects have sequenced DNA from ocean water sampled from around the world [4], microbial communities in and on humans [5-8], and acid drainage from an abandoned mine [9].”
Interaction between the gut microbiome and mucosal immune system (2017, background): “Microbial genome sequences contain 3 × 10(6) genes, which is approximately 150-fold the length of the human genome [1].”
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Associating microbiome composition with environmental covariates using generalized UniFrac distances (2012, methodology): “Distance-based statistical tests have been applied to test the association of microbiome composition with environmental or biological covariates.”
Mash: fast genome and metagenome distance estimation using MinHash (2015, methodology): “For a large-scale test, samples from the Human Microbiome Project [35] (HMP) and Metagenomics of the Human Intestinal Tract [36] (MetaHIT) were combined to create a ~10 TB 888-sample dataset.”
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis (2018, methodology): “The runtime of each metaWRAP ’ s modules was evaluated on a subset of the Human Intestinal Tract (MetaHIT) survey [40].”
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Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics (2015, positive): “DNAwas extracted using theMoBio Powersoil DNA isolation kit (as seen in Qin et al., 2010 and also http://www.mobio.com/soil-dna-isolation/powersoildna-isolation-kit.html).”