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Microbial Co-occurrence Relationships in the Human Microbiome

Figure 3

Global network properties summarizing key microbial hubs and interaction patterns.

A) Node degree distributions of overall, co-occurrence, and co-exclusion associations in the human microbiome. This is well-fit by a power law with slope −1,7 (dotted red regression line, adjusted R2 = 0.9). Node degree indicates the number of links that connect a node to others in the network. Power law degree distributions, referred to as scale-free, mean that most nodes have only a few edges and are often connected by a few high-degree hub nodes. The top five most connected hubs as indicated in callouts, mainly signature oral taxa including Porphyromonas in the tongue dorsum. B) and C) Node proportions after division of the network into body sites (B) or classes (C). Both pie charts show that the composition of the network (in agreement with underlying data) is skewed towards the oral cavity (B) and its constituent Firmicutes (including Bacilli and Clostridia) (C). (B) further agrees with published measures of body sites' alpha diversity [84]. D) and E) Composition of relationships among microbes grouped according to body site (D) and taxonomic class (E). In E), the first two bars (green and red) include the fraction of all possible edges incident to at least one node representing a class or one of its members (root scaled for visualization). The second two bars (lime and orange) only include pairs of microbes that are members of the same class, again normalized as a fraction of total possible interactions and root scaled. The Bacilli, Bacteroidia, and Fusobacteria contain significantly more negatively associated microbes than expected by permutation testing (see Table S2), and classes overall are depleted for negative associations, indicating that members of the same class tend not to compete strongly with each other in these communities.

Figure 3

doi: https://doi.org/10.1371/journal.pcbi.1002606.g003