title: Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.
abstract: Eukaryotic microbes (protists) residing in the vertebrate gut influence host health and disease, but their diversity and distribution in healthy hosts is poorly understood. Protists found in the gut are typically considered parasites, but many are commensal and some are beneficial. Further, the hygiene hypothesis predicts that association with our co-evolved microbial symbionts may be important to overall health. It is therefore imperative that we understand the normal diversity of our eukaryotic gut microbiota to test for such effects and avoid eliminating commensal organisms. We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles and a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota via high-throughput sequencing. To place the human gut microbiota within a broader context our dataset also includes gut samples from diverse mammals and samples from other aquatic and terrestrial environments. We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. However, the eukaryotic microbiota of the western population appears depauperate. The distribution of symbionts found in mammals reflects both host phylogeny and diet. Eukaryotic microbiota in the gut are less diverse and more patchily distributed than bacteria. More broadly, we show that eukaryotic communities in the gut are less diverse than in aquatic and terrestrial habitats, and few taxa are shared across habitat types, and diversity patterns of eukaryotes are correlated with those observed for bacteria. These results outline the distribution and diversity of microbial eukaryotic communities in the mammalian gut and across environments.
authors.affiliation: Biofrontiers Institute, University of Colorado Boulder, CO, USA.
authors.forename: Laura Wegener
authors.initials: LW
authors.lastname: Parfrey
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, CO, USA.
authors.forename: William A
authors.initials: WA
authors.lastname: Walters
authors.affiliation: Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA.
authors.forename: Christian L
authors.initials: CL
authors.lastname: Lauber
authors.affiliation: Biofrontiers Institute, University of Colorado Boulder, CO, USA.
authors.forename: Jose C
authors.initials: JC
authors.lastname: Clemente
authors.affiliation: Biofrontiers Institute, University of Colorado Boulder, CO, USA.
authors.forename: Donna
authors.initials: D
authors.lastname: Berg-Lyons
authors.affiliation: 454 Life Sciences, Roche Company Branford, CT, USA.
authors.forename: Clotilde
authors.initials: C
authors.lastname: Teiling
authors.affiliation: 454 Life Sciences, Roche Company Branford, CT, USA.
authors.forename: Chinnappa
authors.initials: C
authors.lastname: Kodira
authors.affiliation: 454 Life Sciences, Roche Company Branford, CT, USA.
authors.forename: Mohammed
authors.initials: M
authors.lastname: Mohiuddin
authors.affiliation: 454 Life Sciences, Roche Company Branford, CT, USA.
authors.forename: Julie
authors.initials: J
authors.lastname: Brunelle
authors.affiliation: 454 Life Sciences, Roche Company Branford, CT, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Driscoll
authors.affiliation: Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA ; Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA.
authors.forename: Noah
authors.initials: N
authors.lastname: Fierer
authors.affiliation: Department of Ecology and Evolution, University of Chicago Chicago, IL, USA ; Institute of Genomic and Systems Biology, Argonne National Laboratory Argonne, IL, USA.
authors.forename: Jack A
authors.initials: JA
authors.lastname: Gilbert
authors.affiliation: Biofrontiers Institute, University of Colorado Boulder, CO, USA ; Howard Hughes Medical Institute, University of Colorado Boulder, CO, USA.
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
keywords: host-associated eukaryotes; human microbiome; intestinal protozoa; microbial diversity; microbial ecology; parasites; protist; salinity