Uni Frac Comparing Microbial Communities Presented by Donovan

Uni. Frac: Comparing Microbial Communities Presented by: Donovan Parks

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

Why compare microbial communities?

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

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

Uni. Frac: Distance Measures the evolutionary distance between microbial communities n

Uni. Frac: Significance Test n Do two communities differ significantly?

Uni. Frac: Community Distance Matrix

Uni. Frac: Sequence Jackknifing How does the number and evenness of sequences from each community affect the results? n

Weighted Uni. Frac What about the relative abundance of sequences (i. e. , evenness)? n

Uni. Frac: A Practical Look

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

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

References Uni. Frac: Lozupone C, Knight R, Uni. Frac: a New Phylogenetic Method for Comparing Microbial Communities, Appl. Environ. Microbiol. , Vol. 71, December 2005. n Lozupone C, Hamady M, Knight R, Uni. Frac - An Online Tool for Comparing Microbial Community Diversity in a Phylogenetic Context, BMC Bioinformatics, Vol. 7, August 2006. n n Online Tool: http: //bmf 2. 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. n Tree. Climber (source of soil sample example): Schloss PD, Handelsman J, Introducing Tree. Climber, a test to compare microbial community structures, Applied and environmental microbiology, Vol. 72, No. 4. , April 2006. n