Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease
Fig 6
Relationship between embedding space and phylogeny.
A: Hierarchical clustering of ASVs using similarity between property vectors matches phylogenetic tree topology. Histograms (light blue) show branch score distances (A1) and symmetric distances (A2) between permuted phylogenetic trees and hierarchically clustered trees based on property similarity. The dotted red line shows the distance between the true phylogenetic tree and the property-based tree. B: 2D PCoA ordination using cosine distance of 1500 randomly selected ASVs in embedding space. 10 pairs of ASVs were selected based on their high spearman correlation in the American Gut ASV table across all samples(r > 0.7). Each pair is denoted by shape. Color shows the family classification of the selected pairs, and all other ASVs are shown in grey. C: t-SNE ordination using cosine distance of 5000 randomly selected ASVs, colored by genus. 3 genera highlighted in the dashed circle exhibit similar co-occurrence patterns.