SpeSpeNet: A User-Friendly Tool for Constructing and Visualizing Microbiome Networks

SpeSpeNet: A User-Friendly Tool for Constructing and Visualizing Microbiome Networks

Correlation networks are commonly used to explore microbiome data. In these networks, nodes are taxa and edges represent correlations between their abundance patterns across samples. As clusters of correlating taxa (co-abundance clusters) often indicate a shared response to environmental drivers, network visualization contributes to system understanding. Currently, most tools for creating and visualizing co-abundance networks from microbiome data either require the researcher to have coding skills, or they are not user-friendly, with high time expenditure and limited customizability. Furthermore, existing tools lack focus on the association between environmental drivers and the structure of the microbiome, even though many edges in correlation networks can be understood through a shared association of two taxa with the environment. For these reasons we developed SpeSpeNet (Species-Species Network, https://tbb.bio.uu.nl/SpeSpeNet), a practical and user-friendly R-shiny tool to construct and visualize correlation networks from taxonomic abundance tables. The details of data preprocessing, network construction, and visualization are automated, require no programming ability for the web version, and are highly customizable, including associations with user-provided environmental data. Here, we present the details of SpeSpeNet and demonstrate its utility using three case studies.

SpeSpeNet provides an intuitive platform for network analysis of microbiomes, facilitating researchers to uncover complex interactions between microbes and their environments.

Read More: A. L. van Eijnatten et al. SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks. ISME Communications, ycaf036, https://doi.org/10.1093/ismeco/ycaf036

SpeSpeNet co-abundance network of the microbiome in a poly-contaminated city park and the corresponding water treatment plant (Hauptfeld et al)

Nodes are genera and edges are SparCC correlations > 0.63. A) Network colored by taxonomic annotation at the order rank. B) Network colored by Pearson correlation with O2 levels. The bottom-right cluster corresponds to genera preferring lower O2 and the top-left cluster consists of genera that prefer higher O2 levels. C) Network colored by the sampling site in the park/remediation pipeline in which genera were most abundant. The genera in the bottom-right cluster prefer the park side and the microbes in the top-left cluster prefer the plant-side. D) Network colored by k-means cluster assignment with k = 2. The k-means algorithm correctly groups genera into two co-abundance clusters that were already visually obvious. E) Barplot of taxonomic composition at order rank for the co-abundance clusters from D. Colors as in A. F) Distribution of correlation values with O2 for the genera in the clusters from D. Co-abundance cluster 1 shows the microbial community in the park side, and cluster 2 in the plant side of the remediation pipeline. Colors as in A.