Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM)
Fig 4
MicroSLAM identifies novel IBD associations.
We analyzed all 71 species in our IBD compendium for three types of associations with case/control status: relative abundance (Kraken2 + Bracken: amount of the species predicts disease), population structure (microSLAM τ: strain predicts disease), and gene family (microSLAM β: gene presence/absence predicts disease). A) Venn diagram showing the number of species with significant IBD associations of each type. For genes, we counted the species if it had at least one significant gene family; species varied in the number of hits (S2 Table). All tests are localFDR adjusted for multiple testing. B) Boxplots showing the AUC ROC from τ test models for all 71 species, stratified by bacterial class. C) UHGG species tree for all 71 species, colored by order. The τ value, p-value for τ test, number of significant genes, and number of samples for each species are plotted in the outer rings. D) Volcano plot for β tests with significant genes (localFDR < 0.2) colored by bacterial order. (S3 Table) E) Bar plot of COG categories for the 83 genes with significant β tests.