UniFrac: Comparing Microbial Communities Presented by: Donovan Parks
Overview • Motivating example • Quick look at Bray-Curtis Index (BCI) • UniFrac: distance measure, significance test, community tree, sequence jackknifing • Contrast BCI and UniFrac
Bray-Curtis Index (BCI): Distance Measure • Measures the difference in OTU diversity between microbial communities.
BCI: Pros and Cons • Pros: • Simple (both conceptually and experimentally) • Considers both richness and evenness # OTU in a Community Relative Abundance • Cons: • All clusters considered equally different
UniFrac: Distance Measure • Measures the evolutionary distance between microbial communities
UniFrac: Significance Test • Do two communities differ significantly?
UniFrac: Sequence Jackknifing • How does the number and evenness of sequences from each community affect the results?
Weighted UniFrac • What about the relative abundance of sequences (i.e., evenness)?
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
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
References • UniFrac: • 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: http://bmf2.colorado.edu/unifrac/index.psp (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.