title: The convergence of carbohydrate active gene repertoires in human gut microbes.
abstract: The extreme variation in gene content among phylogenetically related microorganisms suggests that gene acquisition, expansion, and loss are important evolutionary forces for adaptation to new environments. Accordingly, phylogenetically disparate organisms that share a habitat may converge in gene content as they adapt to confront shared challenges. This response should be especially pronounced for functional genes that are important for survival in a particular habitat. We illustrate this principle by showing that the repertoires of two different types of carbohydrate-active enzymes, glycoside hydrolases and glycosyltransferases, have converged in bacteria and archaea that live in the human gut and that this convergence is largely due to horizontal gene transfer rather than gene family expansion. We also identify gut microbes that may have more similar dietary niches in the human gut than would be expected based on phylogeny. The techniques used to obtain these results should be broadly applicable to understanding the functional genes and evolutionary processes important for adaptation in many environments and useful for interpreting the large number of reference microbial genome sequences being generated for the International Human Microbiome Project.
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Lozupone
authors.forename: Micah
authors.initials: M
authors.lastname: Hamady
authors.forename: Brandi L
authors.initials: BL
authors.lastname: Cantarel
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Coutinho
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Jeffrey I
authors.initials: JI
authors.lastname: Gordon
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D002241:Carbohydrates / Q000096:biosynthesis / Q000235:genetics; D016000:Cluster Analysis; D022761:Gene Transfer, Horizontal; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D014644:Genetic Variation; D006026:Glycoside Hydrolases / Q000235:genetics*; D016695:Glycosyltransferases / Q000235:genetics*; D006801:Humans; D007422:Intestines / Q000382:microbiology*; D005810:Multigene Family; D010802:Phylogeny
chemical_list: D002241:Carbohydrates; D016695:Glycosyltransferases; D006026:Glycoside Hydrolases