Microbial Co-occurrence Relationships in the Human Microbiome
Figure 6
Functional and phylogenetic similarities between co-occurring microbes.
Evolutionary (phylogenetic) distances among microbial clades were compared to the clades' functional potentials as defined by the Jaccard index of orthologous gene (COG) families shared between genomes (see Methods). Each point represents a pair of significantly associated microbes colored by direction of the association (green positive, red negative) and shaped by the type of relationship (triangle: between body sites, square: within site). Phylogenetic distances were inferred by FastTree [82] using species-level 16S sequences. Most interactions lie along the diagonal, reflecting the baseline correlation between these functional and evolutionary distances, with highly related clades co-occurring among related habitats (e.g. bilateral skin sites, proximal oral sites) in the lower left. Off-diagonal examples include potential competition among dominant gut signature taxa (e.g. Prevotellaceae/Bacteroides) and functional complementarity between distinct oral pathogens (e.g. Treponema/Prevotella).