High-throughput sequencing technologies provide new opportunities to address longstanding questions about habitat adaptation in microbial organisms. How have microbes managed to adapt to such a wide range of environments, and what genomic features allow for such adaptation? We review recent large-scale studies of habitat adaptation, with emphasis on those that utilize phylogenetic techniques. On the basis of current trends, we summarize methodological challenges faced by investigators, and the tools, techniques and analytical approaches available to overcome them. Phylogenetic approaches and detailed information about each environmental sample will be crucial as the ability to collect genome sequences continues to expand.
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The authors would like to thank Mike Robeson for useful comments on the draft. The work from our laboratory described in this review was supported in part by the National Institutes of Health, the Crohn's and Colitis Foundation of America, the Bill and Melinda Gates Foundation, and the Howard Hughes Medical Institute.