Fig. 1

HIV-infected pneumonia patient stool and BAL exhibit body habitat specificity. a Principal coordinates analysis (PCoA) using Bray–Curtis dissimilarity of n = 271 bronchoalveolar lavage (BAL; n = 125) and stool (n = 146) bacterial community profiles (including 120 paired BAL–stool samples) representatively rarefied to 51,997 reads/sample. b Mean difference in reads/sample is plotted for the top 30 taxa differentiating BAL and stool bacterial communities, identified using linear mixed effects model and false discovery rate q < 0.05, read difference ≥ 100, and presence in ≥ 50% of the enriched group. PC, principal coordinate; taxa in green were also within the top 30 random forest predictive taxa differentiating BAL and stool samples