Science has a section dedicated to Microbial Ecology including a review describing microbial biogeography studying communities on the basis of trait rather than taxonomic diversity. Certainly this interlinks with metagenomic approaches well, something I’ve been thinking about more after visiting some of the folks at Montana State Thermal Biology Institute and all the increasingly massive datasets like what CAMERA provides.
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The EU-funded project MetaHIT (Metagenomics of the Human Intestinal Tract) has an official website available at: http://www.metahit.eu