title: Phylogenetics and the human microbiome.
abstract: The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.
authors.affiliation: Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 91802, USA matsen@fhcrc.org.
authors.forename: Frederick A
authors.initials: FA
authors.lastname: Matsen
mesh_terms: D001419:Bacteria / Q000235:genetics; D006801:Humans; D064307:Microbiota / Q000235:genetics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: 16S; human microbiome; human microbiota; metagenome; microbial ecology; phylogenetic methods
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