Metagenomics is a complex of research methodologies aimed at characterizing microbial communities and cataloging microbial diversity and distribution without isolating or culturing organisms. This approach will unavoidably engender new ways of thinking about microbial ecology that supplant the concept of “species.” This concept—thanks to comparative genomics—has in any case become increasingly unsustainable, either as a way of binning diversity or as a biological reality. Communities will become the units of evolutionary and ecological study. Although metagenomic methods will increasingly find uses in protistology and mycology, the emphasis so far has been, and our focus here will be, on prokaryotes (bacteria and archaea).