Figure 3: Unsupervised clustering approaches revealed differences in bacterial alpha diversity and composition in three body compartments of critically ill patients.

Panels A-D demonstrate bacterial Dirichlet Multinomial Mixture (DMM) modeling results for each compartment separately. DMM clusters had significant differences in alpha diversity (A) and composition (obligate anaerobe abundance in shown in panel B and pathogen abundance shown in panel C), with cluster 3 in each compartment showing very low Shannon Index and enrichment for pathogens (Low-Diversity cluster). Oral and lung cluster assignments were strongly associated (Odds ratio for assignment to the Low-Diversity cluster: 9.74 (5.61-17.29), p<0.0001), whereas lung and gut cluster assignments were less strongly but significantly associated (panel D).