Functional Metagenomic Investigations of the Human Intestinal Microbiota

Center for Genome Sciences and Systems Biology, Washington University School of Medicine St. Louis, MO, USA.
Frontiers in Microbiology (Impact Factor: 3.94). 10/2011; 2:188. DOI: 10.3389/fmicb.2011.00188
Source: PubMed

ABSTRACT The human intestinal microbiota encode multiple critical functions impacting human health, including metabolism of dietary substrate, prevention of pathogen invasion, immune system modulation, and provision of a reservoir of antibiotic resistance genes accessible to pathogens. The complexity of this microbial community, its recalcitrance to standard cultivation, and the immense diversity of its encoded genes has necessitated the development of novel molecular, microbiological, and genomic tools. Functional metagenomics is one such culture-independent technique, used for decades to study environmental microorganisms, but relatively recently applied to the study of the human commensal microbiota. Metagenomic functional screens characterize the functional capacity of a microbial community, independent of identity to known genes, by subjecting the metagenome to functional assays in a genetically tractable host. Here we highlight recent work applying this technique to study the functional diversity of the intestinal microbiota, and discuss how an approach combining high-throughput sequencing, cultivation, and metagenomic functional screens can improve our understanding of interactions between this complex community and its human host.

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Available from: Gautam Dantas, Jul 24, 2015
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    • "These largely sequencing-driven studies , along with mechanistic studies in vitro and in animal models, have emphasized the role the human microbiome plays in health and disease, including inflammatory bowel disease (IBD), metabolic syndrome, autoimmune disorders, and even cancer. Here, in this " Research Topic " collection of reviews, perspectives , and original research articles, leading researchers in the field have highlighted recent developments in our appreciation of the structure and function of the human microbiome, spanning a wide range of topics including immune development (Derrien et al., 2011; Kosiewicz et al., 2011; Pfeiffer and Sonnenburg, 2011; Reading and Kasper, 2011; Smith and Garrett, 2011), IBD (Young et al., 2011), nutrition, and obesity (Geurts et al., 2011; Li et al., 2011; Lin, 2011; Thomas et al., 2011), and novel methods for analyzing complex microbial communities (Moore et al., 2011; Parfrey et al., 2011). First, we present a series of reviews highlighting that the human immune system is intimately linked to the gut microbiome; the gut microbiota influences immune development, susceptibility to infection from pathogens, and inflammation (Kosiewicz et al., 2011; "
    Frontiers in Microbiology 09/2011; 2:190. DOI:10.3389/fmicb.2011.00190 · 3.94 Impact Factor
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