Molecular Ecological Network Analyses
(MENA)
Ye Deng, Ph.D
Postdoctoral Research Associate
Institute of Environmental Genomics
The University of Oklahoma
May, 2011
INSTITUTE FOR ENVIRONMENTAL GENOMICS
UNI V E R S I T Y OF OKL A HOM A
From parts to interactions
Microbial species richness
Species diversity
Species network
intro
RMT
Species abundance
Different species
Species interactions
analysis
Adjacent matrix:
Simpson index:
concln
S = The number of
different species
Shannon index:
…
Conventional methods: Shannon diversity indexes
•
•
Species number and abundance of each species
http://ieg2.ou.edu/MENA
Ignore interactions among different species
Molecular Ecological network construction
intro
High throughput sequencing data (e.g.
16S pyrosequencing) or Microarray data
RMT
Standardized relative abundance (SRA)
of sequence numbers in a community
analysis
concln
Pair-wise similarity of gene abundance
across different samples: e.g. Pearson
correlation
Determination of adjacency matrix by
RMT-based approach
http://ieg2.ou.edu/MENA
The RMT-based network construction
intro
RMT
analysis
concln
Luo, Yang et al. BMC Bioinformatics, 2007, 8:299.
http://ieg2.ou.edu/MENA
The RMT-based network construction
intro
RMT
analysis
concln
• Each node indicates a OTU / species and different colors demonstrate the
genus they belong to
• The edge indicates the interaction between the linkedhttp://ieg2.ou.edu/MENA
the OTUs/species
The Molecular Ecological Network analyses
intro
o Overall, what is the network topology?
the general network properties and modular structure
RMT
o For individual species, who are the major players?
the important nodes in the system
analysis
concln
o How does the network work?
the network individuals/modules’ functions
o For multiple networks, what are the differences
between them?
the network comparisons
http://ieg2.ou.edu/MENA
The steps of MENA
intro
Network characterization and
module detection
RMT
Identification of topological roles
of individual nodes
analysis
Eigengene network analyses
concln
Network comparison between
different conditions
Association of network properties
to ecological functional traits
http://ieg2.ou.edu/MENA
Responses of grass ecosystems to elevated CO2
intro
RMT
BioCON (Biodiversity,
CO2, and Nitrogen) at
the University of
Minnesota by Peter
Reich
Elevated
CO2
analysis
concln
Ambient
CO2
Each ring:
20m diameter
There are
296 plots
in total.
Each plot:
2×2m
http://ieg2.ou.edu/MENA
Modular organization of the MEN under ambient CO2
intro
RMT
analysis
concln
•
•
•
Based on 454 sequencing data at ambient CO2.
All the MENs examined were modular, with distinct modules .
A module is a group of OTUs/functional genes that are highly correlated among
themselves, but have few connections with OTUs/functional genes belonging to
http://ieg2.ou.edu/MENA
other modules.
The topological roles of nodes under ambient and
elevated CO2
intro
RMT
analysis
concln
http://ieg2.ou.edu/MENA
Effects of eCO2 on the network interactions of
Actinobacteria
intro
eCO2
aCO2
RMT
analysis
concln
•
•
Top 10 OTUs with the highest connectivity at eCO2 and their
corresponding OTUs at aCO2
More complicated network interactions at eCO2 than aCO2
http://ieg2.ou.edu/MENA
Effects of eCO2 on the network interactions of
Verrucomicrobia
intro
aCO2
eCO2
RMT
analysis
concln
•
Oppositely, the interaction of Verrucomircrobia was much less under
eCO2 than aCO2.
http://ieg2.ou.edu/MENA
Network connectivity vs. the soil geochemical traits
intro
aCO2
Phylogeny
Network
size
RMT
analysis
concln
eCO2
rM
p
Network
size
rM
p
All detected OTUs
292
0.039
0.169
263
0.368
0.001
Acidobacteria
45
0.054
0.262
34
0.137
0.124
Actinobacteria
81
0.381
0.002
76
0.562
0.001
Bacteroidetes
23
-0.084
0.622
24
0.487
0.012
Firmicutes
11
0.023
0.338
8
0.310
0.114
Gemmatimonadetes
10
-0.220
0.958
8
0.299
0.168
Planctomycetes
4
0.604
0.221
5
-0.651
1.000
α-Proteobacteria
45
-0.034
0.638
42
0.472
0.001
β-Proteobacteria
22
0.029
0.319
24
0.297
0.044
δ-Proteobacteria
6
0.498
0.138
8
0.043
0.416
γ-Proteobacteria
11
-0.159
0.723
9
0.020
0.399
Verrucomicrobia
12
0.184
0.057
9
0.086
0.253
http://ieg2.ou.edu/MENA
Conclusion
intro
RMT
analysis
concln
o The high-throughput metagenomic data provide a
great opportunity to study the microbial interactions
in a large scale
o The network analysis can help to identify the key
species, compare community structure under
different treatments, and link the network topology
with environmental traits
o Elevated CO2 dramatically altered the network
interactions, indicating the switch of microbial
community
http://ieg2.ou.edu/MENA
Acknowledgement
intro
RMT
o
o
o
o
o
Jizhong (Joe) Zhou
Zhili He
Liyou Wu
Feng Luo
Yunfeng Yang
analysis
concln
Funding Source:
o US Department of Energy
o United States Department of Agriculture
Welcome to our online MENA pipeline: http://ieg2.ou.edu/MENA
http://ieg2.ou.edu/MENA