title: Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation.
abstract: 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.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.
authors.forename: Jesse R R
authors.initials: JR
authors.lastname: Zaneveld
authors.forename: Laura Wegener
authors.initials: LW
authors.lastname: Parfrey
authors.forename: Will
authors.initials: W
authors.lastname: Van Treuren
authors.forename: Catherine
authors.initials: C
authors.lastname: Lozupone
authors.forename: Jose C
authors.initials: JC
authors.lastname: Clemente
authors.forename: Dan
authors.initials: D
authors.lastname: Knights
authors.forename: Jesse
authors.initials: J
authors.lastname: Stombaugh
authors.forename: Justin
authors.initials: J
authors.lastname: Kuczynski
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D001105:Archaea / Q000235:genetics / Q000502:physiology*; D001419:Bacteria / Q000235:genetics; D018407:Bacterial Physiological Phenomena; D017753:Ecosystem; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D010802:Phylogeny; D017422:Sequence Analysis, DNA