1. UniFrac: Comparing Microbial Communities
Presented by:
Donovan Parks

2. Overview Motivating example Quick look at Bray-Curtis Index (BCI)
UniFrac: distance measure, significance test, community tree, sequence jackknifing
Contrast BCI and UniFrac

3. Why compare microbial communities?

4. Bray-Curtis Index (BCI): Distance Measure
Measures the difference in OTU diversity between microbial communities.

5. BCI: Pros and Cons Pros: Cons:
Simple (both conceptually and experimentally)
Considers both richness and evenness
# OTU in a
Community
Relative
Abundance
Cons:
All clusters considered equally different

6. UniFrac: Distance Measure
Measures the evolutionary distance between microbial communities

7. UniFrac: Significance Test
Do two communities differ significantly?

8. UniFrac: Community Distance Matrix

9. UniFrac: Sequence Jackknifing
How does the number and evenness of sequences from each community affect the results?

10. Weighted UniFrac
What about the relative abundance of sequences (i.e., evenness)?

11. UniFrac: A Practical Look

12. Final Remarks: BCI vs. UniFrac
They are different, equally valid measures!
BCI: taxon-based method which considers richness and evenness
UniFrac: phylogenetic-based method which considers evolutionary divergence
Which to prefer depends on the questions you are trying to answer

13. Final Remarks: Many Ways to Compare
Many richness and evenness measures (e.g., Jaccard, Sörensen)
Other phylogenetic distance measures (e.g., TreeClimber)
Many interesting and meaningful ways to compare microbial communities:
Richness and evenness
Evolutionary divergence
Functional diversity

14. References UniFrac: BCI: TreeClimber (source of soil sample example):
Lozupone C, Knight R, UniFrac: a New Phylogenetic Method for Comparing Microbial Communities, Appl. Environ. Microbiol., Vol. 71, December 2005.
Lozupone C, Hamady M, Knight R, UniFrac - An Online Tool for Comparing Microbial Community Diversity in a Phylogenetic Context, BMC Bioinformatics, Vol. 7, August 2006.
Online Tool: (excellent help page)
BCI:
Bray R, Curtis T, An Ordination of the Upland Forest Communities of Southern Wisconsin, Ecological Monographs, Vol. 27, 1957.
TreeClimber (source of soil sample example):
Schloss PD, Handelsman J, Introducing TreeClimber, a test to compare microbial community structures, Applied and environmental microbiology, Vol. 72, No. 4., April 2006.