TY - JOUR
T1 - Improving the Inference of Co-occurrence Networks in the Bovine Rumen Microbiome
AU - Zheng, Huiru
AU - Wang, Haiying / HY
AU - Dewhurst, Richard
AU - Roehe, Rainer
PY - 2018/11/2
Y1 - 2018/11/2
N2 - The importance of the composition and signature of rumen microbial communities has gained increasing attention. One of the key techniques was to infer co-abundance networks through correlation analysis based on relative abundances. In this study, we proposed the use of a framework including a compendium of two correlation measures and three dissimilarity metrics to mitigate the compositional effect in the inference of significant associations in the bovine rumen microbiome. We tested the framework on rumen microbiome data including both 16S rRNA and KEGG genes associated with methane production in cattle. Based on the identification of significant positive and negative associations supported by multiple metrics, two co-occurrence networks, e.g. co-presence and mutual-exclusion networks, were constructed. Significant modules associated with methane emissions were identified. In comparison to previous studies, our analysis demonstrates that deriving microbial associations based on the correlations between relative abundances may not only lead to missing information but also produce spurious associations. To bridge together different co-presence and mutual-exclusion relations, a multiplex network model has been proposed for integrative analysis of co-occurrence networks which has great potential to support the prediction of animal phytotypes and to provide additional insights into biological mechanisms of the microbiome associated with the traits.
AB - The importance of the composition and signature of rumen microbial communities has gained increasing attention. One of the key techniques was to infer co-abundance networks through correlation analysis based on relative abundances. In this study, we proposed the use of a framework including a compendium of two correlation measures and three dissimilarity metrics to mitigate the compositional effect in the inference of significant associations in the bovine rumen microbiome. We tested the framework on rumen microbiome data including both 16S rRNA and KEGG genes associated with methane production in cattle. Based on the identification of significant positive and negative associations supported by multiple metrics, two co-occurrence networks, e.g. co-presence and mutual-exclusion networks, were constructed. Significant modules associated with methane emissions were identified. In comparison to previous studies, our analysis demonstrates that deriving microbial associations based on the correlations between relative abundances may not only lead to missing information but also produce spurious associations. To bridge together different co-presence and mutual-exclusion relations, a multiplex network model has been proposed for integrative analysis of co-occurrence networks which has great potential to support the prediction of animal phytotypes and to provide additional insights into biological mechanisms of the microbiome associated with the traits.
KW - Compositional data
KW - co-occurrence networks
KW - rumen microbiome
KW - methane emission
UR - https://pure.ulster.ac.uk/en/publications/improving-the-inference-of-co-occurrence-networks-in-the-bovine-r
U2 - 10.1109/TCBB.2018.2879342
DO - 10.1109/TCBB.2018.2879342
M3 - Article
C2 - 30403635
SN - 1545-5963
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics
M1 - doi: 10.1109/TCBB.2018.2879342
ER -