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
Why compare microbial communities?
Soil suppressing
Tree Pathogens
Soil not suppressing
Tree Pathogens
Is this guy protecting our trees?
Bray-Curtis Index (BCI): Distance Measure
Measures the difference in OTU diversity between
microbial communities.

Cluster
Normalize
0.4
0.3
0.3
Community 1
Cluster
Normalize
0.2
0.4
Cluster
Differences
0.4
Community 2
Clusters defined by taxonomy
or sequence similarity
0.2
0.1
0.1
BCI = 0.4 / 2 = 0.2
Normalize so measure is between [0, 1]
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

Similar Communities
Maximally Different Communities
UniFrac Distance Measure = (------) / (------ + ------)
UniFrac: Significance Test
Do two communities differ significantly?
Randomize Community Labels
Observed Tree
...
# Trees

Magic level of
significance!
UniFrac Distance
UniFrac: Community Distance Matrix
Pairwise Comparison
0
0.6 0.5
UPGMA
0.6
0
0.5 1.0
1.0
0
Distance Matrix
Community Tree
UniFrac: Sequence Jackknifing
How does the number and evenness of sequences from
each community affect the results?

Sequence
Jackknifing
UniFrac
Analysis
Replicate 100
to 1000 times
UniFrac
Analysis
Weighted UniFrac
What about the relative abundance of sequences (i.e.,
evenness)?

Since there are twice as
many -- sequences, they
get half the weight.
UniFrac: A Practical Look
Remove duplicate sequences
if not doing weighted UniFrac.
16S Gene
Sequence
Library
Filter
Sequences
0.7
16S Gene
Sequence
Library
Filter
Sequences
16S Gene
Sequence
Library
Filter
Sequences
Multiple Sequence
Alignment
(e.g., MUSCLE)
Tree Construction
(e.g., RAxML)
UniFrac Analysis
0.8
Tree must be rooted
Tree must have meaningful
branch lengths
Community Tree
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.
