7. Eukaryotic contribution to the human microbiome
• Human health
– Major source of morbidity and mortality
• Ecology
– predation, parasitism, competition
13. Patterson 1999, American Naturalist
70 + lineages,
predominately
microbial
Eukaryotic diversity as of 1999
14. 70+ lineages of eukaryotes
Images from O. Roger Anderson
• Defined by ultrastructural identities
– Characteristic patterns of subcellular organization
• Lineages robust, confirmed by molecular data
15. c Biology
010
oupled with a moderate number of genes has the power to r econstruct deep phylogenetic
t the support for major eukaryotic clades using taxon-rich analyses, including 88–451 taxa
analyzing data fr om up to 16 genes. These analyses reveal remarkable consistency in supported
g levels of missing data (17–69%). Several major gr oups are both stable and strongly supported
ta), while the pr oposed supergroup “Chromalveolata” is rejected. This approach contrasts
aucity of major eukaryotic lineages (19 or fewer). Images ar e of representative organisms and
ity of eukaryotic lineages. All images are from http:/ / www.mbl.edu/ microscope.
and Codominant Multilocus Markers
nig ...................................................................................... ......................................... 491
essing Life-History Evolution in a Fr eshwater Fish Radiation
hristopher P. Burridge, and Graham P. Wallis ............................................ .............. 504
Yield a Well-Resolved Eukaryotic Tree of Life
Yonas I. Tekle, Erica Lasek-Nesselquist, Hilary G. Morrison,
and Laura A. Katz ..................................................................... .................................. 518
c, and Relaxed Clock Methods in a Comparative Genomics
ory of Soybean ( Glycine max)
.................................................................................................................. ................... 534
ntinental Colonization Events during the Rapid
): the Utility of AFLPs versus Mitochondrial and
nt Excoffier, and Gerald Heckel.................................................................................... 548
ee Estimation: Impact of Mutational and Coalescent Ef fects on
ng among Dif ferent Methods
ubatko, and L. Lacey Knowles ............................................................. ....................... 573
lanced Repr esentation of Phylogenetic Topologies
....................................................................................... .............................................. 584
ally Survive the Oligocene Dr owning of New Zealand?
J. Lowe ....................................................................................... .................................. 594
fects on Trait Variance in Clades
........................................................................ ............................................................ 602
uation of Comparative Data, 2nd edition
............................................................................................... ..................................... 608
Viruses
...................................................................................... ............................................... 610
tics and V icariance
s........................................................................................ ........................................... 612
ed on behalf of the Society of Systematic Biologists
http://systbiol.org/
Volume59Number5,pp.491–614October2010oxfordSYSTEMATICBIOLOGY
Systematic Biology
A JOURNAL OF THE
Society of Systematic Biologists
OCTOBER 2010
VOLUME 59
NUMBER 5
ONLINE ISSN 1076-836X
PRINT ISSN 1063-5157
16. Parfrey et al. 2010
451 taxa:
72 lineages – 53 with
Ultrastructural
identities
16 genes, including
ribosomal DNA
23. Data analysis with Qiime
Open source, supported, and freely available (http://qiime.org)
Caporaso et al. 2010 Nature Methods
18S tutorial available (Tony Walters)
24. 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)
25. Tree of Silva eukaryotes
• Tree: backbone defined by 2010
eukaryotic tree + updates
• Database: Silva 108 ribosomal
database. 97% representative
sequences.
27. Challenges of using Silva
• Taxonomy based on NCBI
• 20% listed as uncultured eukaryote
• Not standardized for computational analyses
28. • Collaboration between Silva ribosomal database
(Pelin Yilmaz), ISOP systematics committee and
others with computational or taxonomic expertise.
• Goal: revise classification
– reflect phylogeny
– Take advantage of phylogenetic information
– Interface with computational tools
• Implemented in Silva 111 release
Eukaryotic Taxonomy Working Group
Pelin Yilmaz and Frank Oliver Glockner
http://www.arb-silva.de/projects/eukaryotic-taxonomy/
31. Who lives in the human gut?
http://www.stanford.edu/group/parasites/ParaSites2009/NevinsANDLiu_Giardiasis/NevinsANDLiu_Giardiasis.htm
First 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
+ + =
38. Eukaryotic communities in human microbiome
• Hypothesis: Communities of microbial eukaryotes
follow the same diversity patterns as bacteria.
– Shared diversity patterns: environmental factors stronger
– Different: Biological differences (genetic
architecture, size, population structure) more important
51. Beta diversity of host-associated vs
environmental samples: Eukaryotes
Skin communities
Host-Associated
Environmental
Parfrey et al. in prep
52. Beta diversity of host-associated vs
environmental samples: Eukaryotes
Host-Associated
Environmental
Procrustes and mantel test: Significant correlation (p < .001), but a poor fit
53. Beta diversity of host-associated vs
environmental samples
Procrustes and mantel test: Significant correlation (p < .001), but a poor fit
55. Taxa summaries bacteria:
composition consistent across individuals
Human and other mammal fecal samples
Relativeabundanceoftaxa
Parfrey et al. in prep
57. Eukaryotic communities in the
vertebrate 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
61. Acknowledgements
Collaborators:
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 Metcalf
Matt Gebert
Chris Lauber
Se Jin Song
Laura Katz
Editor's Notes
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?
