Article

Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65

BGI-Shenzhen, Shenzhen 518083, China.
Nature (Impact Factor: 42.35). 03/2010; 464(7285):59-65. DOI: 10.1038/nature08821
Source: PubMed

ABSTRACT 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.

Download full-text

Full-text

Available from: Joel Dore, Aug 29, 2015
9 Followers
 · 
857 Views
    • "Currently , there are two innovative and noninvasive ways of fecal microbial therapy with a promising future in treating or preventing obesity: fecal microbiota transplantation (FMT) and ''synthetic fecal'' transplantation (SFT). FMT has been suggested to potentially re-establish the healthy microbiota in the recipient and to preserve around 1150 functional bacterial species transferred by the healthy donor (Qin et al. 2010; Zhang et al. 2012). As explained by Zhang et al. (2012), the practice of FMT is not new, since evidence indicates the use of human fecal slurries in patients suffering from severe diarrhea or food poisoning by Ge Hong, a well-known traditional doctor during the fourth century in China. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Recently, a great deal of interest has been expressed regarding strategies to tackle worldwide obesity because of its accelerated wide spread accompanied with numerous negative effects on health and high costs. Obesity has been traditionally associated with an imbalance in energy consumed when compared to energy expenditure. However, growing evidence suggests a less simplistic event in which gut microbiota plays a key role. Obesity, in terms of microbiota, is a complicated disequilibrium that presents many unclear complications. Despite this, there is special interest in characterizing compositionally and functionally the obese gut microbiota with the help of in vitro, animal and human studies. Considering the gut microbiota as a factor contributing to human obesity represents a tool of great therapeutic potential. This paper reviews the use of antimicrobials, probiotics, fecal microbial therapy, prebiotics and diet to manipulate obesity through the human gut microbiota and reveals inconsistencies and implications for future study.
    Genes & Nutrition 07/2015; 10(4):472. DOI:10.1007/s12263-015-0472-4 · 3.42 Impact Factor
  • Source
    • "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. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Metagenomics is a powerful approach to study genetic content of environmental samples that has been strongly promoted by NGS technologies. To cope with massive data involved in modern metagenomic projects, recent tools [3, 35] rely on the analysis of k-mers shared between the read to be classified and sampled reference genomes. Within this general framework, we show in this work that spaced seeds provide a significant improvement of classification capacity as opposed to traditional contiguous k-mers. We support this thesis through a series a different computational experiments, including simulations of large-scale metagenomic projects.
    Bioinformatics 07/2015; DOI:10.1093/bioinformatics/btv419 · 4.62 Impact Factor
  • Source
    • "The gut microbiota was a complicated ecosystem that resides in the host gastrointestinal tract. The gut microbiome (the collective genomes of the gut microbes) encodes 3.3 million non-redundant genes and is 150 times larger than the human gene complement, with most of these genes having unknown functions (Qin et al., 2010). Recent evidences suggested that gut microbiota affect many aspects of host physiology, including the diet, vitamin production, drug metabolism, disease pathogenesis, and the regulation of the immune system (Xu et al., 2013), as well as the metabolism of pharmaceuticals, heavy metals, and organic chemicals (Breton et al., 2013; Clayton et al., 2009). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Neochamaejasmin A, isolated from Stellera chamaejasme L., has been widely used in China. Gut microbiota represent the first barrier against xenobiotics. This study aimed to evaluate the effects of subchronic exposure to neochamaejasmin A on the composition of gut microbiota. We found that neochamaejasmin A altered 21 OTUs in female rats and 46 OTUs in male rats. Among these OTUs, OTU86, OTU338 and OTU482 were shared in neochamaejasmin A-fed groups in both genders, implying that neochamaejasmin A might promote the growth of these three genera. In contrast, little or no effect on 226 OTUs was observed at all doses in both genders, suggesting their resistance to neochamaejasmin A. These findings could help improve our understanding of the health effects of neochamaejasmin A and provide an example of the risk assessment of pharmaceuticals or food contaminants on the gut microbiota composition. Copyright © 2015 Elsevier B.V. All rights reserved.
    Environmental Toxicology and Pharmacology 03/2015; 39(2). DOI:10.1016/j.etap.2015.03.005 · 2.08 Impact Factor
Show more