Parfrey smbe euk_2013_final

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  • Microbes play essential roles in the biogeochemical cycles and nutrient cycling in addition to making up a huge portion of the biomass and biodiversity on our planet.
  • Still not right but maybe closer. Alternate: A phylogenetic framework for understanding the host associated eukaryotes, and other aspects of eukaryotic biology?
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  • Parfrey smbe euk_2013_final

    1. 1. Laura Wegener ParfreyRob Knight, University of ColoradoHost-associated eukaryoticcommunities
    2. 2. We live in a microbial worldEukaryotaArchaeaBacteriaDerived from Woese et al. 1990
    3. 3. EukaryotaArchaeaBacteriaWoese et al. 1990
    4. 4. versusHuman cells andgenesCells GenesProportionhumanModified from Hamady 2008Microbes are dominant closer to home as well
    5. 5. They influence many aspects of our lives
    6. 6. What about eukaryotes?Adl et al 2012
    7. 7. Eukaryotic contribution to the human microbiome• Human health– Major source of morbidity and mortality• Ecology– predation, parasitism, competition
    8. 8. What is a normal/healthy community?
    9. 9. A phylogenetic framework providesthe context for understandingeukaryotic communities
    10. 10. Perspectives on eukaryotic diversityWhittaker 1969
    11. 11. StramenopilesApicomplexaDinoflagellatesCiliatesHaptophytesGreen algae (including plants)TelonemaCentroheliozoaRed algaeCryptomonads + KathablepharidsEuglenozoaHeterolobosea + JakobidsPreaxostylaMalawimonasFornicataParabasaliaEntamoebidaeMastigamoebidaeTubulineaThecamoebidaeAcanthamoebidaeFlabellineaEumycetozoaBreviataAncyromonasApusomonadsFungiMesomycetozoaAnimalsChoanoflagellatesGlaucocystophytesHaplosporidia, Plasmodiophora,Vampyrellids, GromiaForaminifera, Acantharea,Polycystineacore Cercozoa
    12. 12. Patterson 1999, American Naturalist70 + lineages,predominatelymicrobialEukaryotic diversity as of 1999
    13. 13. 70+ lineages of eukaryotesImages from O. Roger Anderson• Defined by ultrastructural identities– Characteristic patterns of subcellular organization• Lineages robust, confirmed by molecular data
    14. 14. c Biology010oupled with a moderate number of genes has the power to r econstruct deep phylogenetict the support for major eukaryotic clades using taxon-rich analyses, including 88–451 taxaanalyzing data fr om up to 16 genes. These analyses reveal remarkable consistency in supportedg levels of missing data (17–69%). Several major gr oups are both stable and strongly supportedta), while the pr oposed supergroup “Chromalveolata” is rejected. This approach contrastsaucity of major eukaryotic lineages (19 or fewer). Images ar e of representative organisms andity of eukaryotic lineages. All images are from http:/ / www.mbl.edu/ microscope.and Codominant Multilocus Markersnig ...................................................................................... ......................................... 491essing Life-History Evolution in a Fr eshwater Fish Radiationhristopher P. Burridge, and Graham P. Wallis ............................................ .............. 504Yield a Well-Resolved Eukaryotic Tree of LifeYonas I. Tekle, Erica Lasek-Nesselquist, Hilary G. Morrison,and Laura A. Katz ..................................................................... .................................. 518c, and Relaxed Clock Methods in a Comparative Genomicsory of Soybean ( Glycine max).................................................................................................................. ................... 534ntinental Colonization Events during the Rapid): the Utility of AFLPs versus Mitochondrial andnt Excoffier, and Gerald Heckel.................................................................................... 548ee Estimation: Impact of Mutational and Coalescent Ef fects onng among Dif ferent Methodsubatko, and L. Lacey Knowles ............................................................. ....................... 573lanced Repr esentation of Phylogenetic Topologies....................................................................................... .............................................. 584ally Survive the Oligocene Dr owning of New Zealand?J. Lowe ....................................................................................... .................................. 594fects on Trait Variance in Clades........................................................................ ............................................................ 602uation of Comparative Data, 2nd edition............................................................................................... ..................................... 608Viruses...................................................................................... ............................................... 610tics and V icariances........................................................................................ ........................................... 612ed on behalf of the Society of Systematic Biologistshttp://systbiol.org/Volume59Number5,pp.491–614October2010oxfordSYSTEMATICBIOLOGYSystematic BiologyA JOURNAL OF THESociety of Systematic BiologistsOCTOBER 2010VOLUME 59NUMBER 5ONLINE ISSN 1076-836XPRINT ISSN 1063-5157
    15. 15. Parfrey et al. 2010451 taxa:72 lineages – 53 withUltrastructuralidentities16 genes, includingribosomal DNA
    16. 16. Current perspective of eukaryotic diversityImages from Micro*scope and Saldarriaga
    17. 17. Does this perspective matter?
    18. 18. Example 1 – MitosisVazquez, Parfrey, Katz 2010Is this universal?
    19. 19. Vazquez, Parfrey, Katz 2010
    20. 20. Mitosis in EukaryotesVazquez, Parfrey, Katz 2010
    21. 21. Integrating eukaryotes into microbialcommunity analyses
    22. 22. Data analysis with QiimeOpen source, supported, and freely available (http://qiime.org)Caporaso et al. 2010 Nature Methods18S tutorial available (Tony Walters)
    23. 23. Marker gene – ribosomal DNA• Ribosomal DNA is universally present• Sequenced for the broadest sample of taxa• Mix of conserved and variable regions• Target SSU-rDNA (18S)
    24. 24. Tree of Silva eukaryotes• Tree: backbone defined by 2010eukaryotic tree + updates• Database: Silva 108 ribosomaldatabase. 97% representativesequences.
    25. 25. Eukaryotic databaseSilva ribosomal databasehttp://www.arb-silva.de/
    26. 26. Challenges of using Silva• Taxonomy based on NCBI• 20% listed as uncultured eukaryote• Not standardized for computational analyses
    27. 27. • Collaboration between Silva ribosomal database(Pelin Yilmaz), ISOP systematics committee andothers with computational or taxonomic expertise.• Goal: revise classification– reflect phylogeny– Take advantage of phylogenetic information– Interface with computational tools• Implemented in Silva 111 releaseEukaryotic Taxonomy Working GroupPelin Yilmaz and Frank Oliver Glocknerhttp://www.arb-silva.de/projects/eukaryotic-taxonomy/
    28. 28. Curated Silva tree
    29. 29. Eukaryotic communities in human microbiome
    30. 30. Who lives in the human gut?http://www.stanford.edu/group/parasites/ParaSites2009/NevinsANDLiu_Giardiasis/NevinsANDLiu_Giardiasis.htmFirst description of Giardia:“I have sometimes also seen tiny creatures moving very prettily…and their belly, which was flattish, furnished with sundry little paws…”-- van Leeuwenhoek 1681+ + =
    31. 31. http://www.stanford.edu/group/parasites/ParaSites2009/NevinsANDLiu_Giardiasis/NevinsANDLiu_Giardiasis.htmEukaryotes in thehuman gut
    32. 32. Eukaryotic parasites
    33. 33. But not all are pathogenic• Commensals
    34. 34. But not all are pathogenic• Commensals• Variation in pathogenicity even in parasites
    35. 35. Eukaryotes are also beneficialDigestion of cellulose in termites and ruminants
    36. 36. http://www.stanford.edu/group/parasites/ParaSites2009/NevinsANDLiu_Giardiasis/NevinsANDLiu_Giardiasis.htmWhat is a normal/healthycommunity?
    37. 37. Eukaryotic communities in human microbiome• Hypothesis: Communities of microbial eukaryotesfollow the same diversity patterns as bacteria.– Shared diversity patterns: environmental factors stronger– Different: Biological differences (geneticarchitecture, size, population structure) more important
    38. 38. Host-associated bacterial communitiesdistinct from environmental communitiesLey, Lozupone et al. 2008, Nature Reviews Microbiol
    39. 39. Few bacterial lineages are host-associatedBacteria foundonly in theenvironmentBacteria found inhumans and otheranimal hostsLey et al 2006
    40. 40. But these few are very successfulLey et al 2008; Image Wikipedia
    41. 41. Parfrey, Walters, Knight 2011Vertebrate-associatedlineagesaccording toparasitological literatureBlastocystisCryptosporidiumBalantidiumTrichomonas,DientamoebaGiardiaEnteromonasChilomastixEntamoebaCandidaEnterocytozoonAscarisPneumocystis
    42. 42. Parfrey, Walters, Knight 2011BlastocystisCryptosporidiumBalantidiumTrichomonas,DientamoebaGiardiaEnteromonasChilomastixEntamoebaCandidaEnterocytozoonAscarisPneumocystis
    43. 43. Parfrey, Walters, Knight 2011BlastocystisCryptosporidiumBalantidiumTrichomonas,DientamoebaGiardiaEnteromonasChilomastixEntamoebaCandidaEnterocytozoonAscarisPneumocystis
    44. 44. Comparison of eukaryotic communities:Dataset
    45. 45. DatasetEnvironmentalSoil, water, lichen, air75 samples65017 readsHost-associatedFecal samples(mammals)Human skin51 samples25574 readsTotal:126 samples90591 reads4092 OTUs
    46. 46. Comparison of eukaryotic communities:DatasetThe bacterial communities in thesesamples were also sequenced toenable direct comparison.
    47. 47. Representative sequences placed in the eukaryotic tree• RAxML EPA placementalgorithm
    48. 48. Alveolates4092 representativesequences within inSilva eukaryotic treeframework
    49. 49. Host-AssociatedEnvironmental
    50. 50. Beta diversity of host-associated vsenvironmental samples: EukaryotesSkin communitiesHost-AssociatedEnvironmentalParfrey et al. in prep
    51. 51. Beta diversity of host-associated vsenvironmental samples: EukaryotesHost-AssociatedEnvironmentalProcrustes and mantel test: Significant correlation (p < .001), but a poor fit
    52. 52. Beta diversity of host-associated vsenvironmental samplesProcrustes and mantel test: Significant correlation (p < .001), but a poor fit
    53. 53. What factors account for differencebetween bacteria and eukaryotes?
    54. 54. Taxa summaries bacteria:composition consistent across individualsHuman and other mammal fecal samplesRelativeabundanceoftaxaParfrey et al. in prep
    55. 55. Taxa summaries eukaryotes:higher variabilityRelativeabundanceoftaxaHuman and other mammal fecal samplesParfrey et al. in prep
    56. 56. Eukaryotic communities in thevertebrate gut• Eukaryote distribution is patchy• Few lineages of eukaryotes are host-associated• Same lineages found across vertebrate taxa (e.g.Blastocystis and Entamoeba)Parfrey et al 2011; Parfrey et al. in prep
    57. 57. “Parasites” = normal?
    58. 58. RelativeabundanceoftaxaHuman and other mammal fecal samplesParfrey et al. in prep“Parasites” = normal?Entamoeba
    59. 59. http://www.stanford.edu/group/parasites/ParaSites2009/NevinsANDLiu_Giardiasis/NevinsANDLiu_Giardiasis.htmJust beginning to elucidate the normalhuman microbiome
    60. 60. AcknowledgementsCollaborators:Valerie McKenzie (CU)Greg Caporaso (NAU)Jack Gilbert (Argonne)Maria Gloria Dominguez (NYU)Dan Lahr (USP)Tim Marques (USP)Orin Shanks (EPA)Rob Knight (CU)Knight Lab:Jessica MetcalfMatt GebertChris LauberSe Jin SongLaura Katz

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