Fig. 3: New cross-feeding interactions predicted by GutCP.
From: Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
a Concise matrix representation of the improved cross-feeding network of the gut microbiome predicted by GutCP (the trajectory example in Fig. 2a with the best performance). The rows are metabolites, and columns, microbial species. Faded cells represent the original, known set of cross-feeding interactions, both production (light blue), consumption (light red), and bidirectional links (gray). The new cross-feeding interactions predicted by GutCP are shown in dark colors: production links in dark blue, consumption links in dark red, and bidirectional links in black. b Network of 293 new links predicted by GutCP (with a P value < 10−3, one-sided binomial test) during 100 independent simulations. Blue nodes represent metabolites, orange is bacteria as in Fig. 1. The size of each node represents its degree. The color of the links is the same as in (a), while the color intensity and link thickness are proportional to the link’s confidence, or P value. For bidirectional links, we represent the direction as that of the link with the smaller P value.
