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Annu Rev Microbiol. 2013;67:459-75. doi: 10.1146/annurev-micro-092412-155642.

Experimental approaches for defining functional roles of microbes in the human gut.

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Center for Genome Sciences & Systems Biology and Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri 63108; email:


The complex and intimate relationship between humans and their gut microbial communities is becoming less obscure, due in part to large-scale gut microbial genome-sequencing projects and culture-independent surveys of the composition and gene content of these communities. These studies build upon, and are complemented by, experimental efforts to define underlying mechanisms of host-microbe interactions in simplified model systems. This review highlights the intersection of these approaches. Experimental studies now leverage the advances in high-throughput DNA sequencing that have driven the explosion of microbial genome and community profiling projects, and the loss-of-function and gain-of-function strategies long employed in model organisms are now being extended to microbial genes, species, and communities from the human gut. These developments promise to deepen our understanding of human gut host-microbiota relationships and are readily applicable to other host-associated and free-living microbial communities.

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