Fig. 3From: Gut microbiota in HIV–pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunctionStool microbiota composition is related to clinical and immunological factors and to CD4 status of HIV-infected pneumonia patients. a Unsupervised hierarchical clustering (using Bray–Curtis dissimilarity (BC) and Ward 2 clustering) and abundance heat map of the top 20 bacterial families present in at least one sample at ≥ 3% relative abundance (ordered from highest to lowest abundance) indicate patterns of microbial co-colonization in stool. b Principal coordinates analysis (PCoA) of BC dissimilarity for n = 106 stool samples illustrates that dominant bacterial family explains a high degree of variation in bacterial microbiota composition [PERMANOVA, R2 = 0.319, p < 0.001; other = Streptococcaceae (covered by Enterococcaceae on left) and Porphyromonadaceae]. Mortality at hospital discharge is significantly associated with c stool Shannon’s diversity (Mann–Whitney U test, p < 0.01) and d CD4 count (cells μl−1; Mann–Whitney U test; p < 0.01). e CD4 count (cells μl−1) is significantly related to stool dominant bacterial family (Mann–Whitney U test; KW, p = 0.02; only families with > 2 samples are included in this analysis). f CD4 count (quartile 1 versus 4) is significantly related to stool Faith’s phylogenetic diversity. Similarity between lower airway and stool samples (Bray–Curtis paired distance) is significantly related to g mortality at hospital discharge (MW, p = 0.01) and h to stool Faith’s phylogenetic diversity (MW, p < 0.03) when grouped by quartiles and quartile 1 versus 4 are compared. PC, principal coordinate; PERMANOVA, permutational multivariate ANOVA; MW, Mann–Whitney U testBack to article page