FIGURE 3.

Bacterial composition and difference between HIV-1-antiretroviral therapy (ART) individuals (cases) and HIV-1-negative controls. (A) Taxonomic tree of bacterial taxa identified in this study. Each dot represents a taxonomic entity. From the inner to outer circles, the taxonomic levels range from phylum to species. Different colors of dots indicate different taxonomy levels according to the color key shown. Numbers in parentheses indicate the total number of unique taxonomies at each taxonomic level. (B,C) Barplots of main bacterial taxa at family and genus levels between cases and controls (average abundance >1% in either group). Main taxa at order level are shown in Supplementary Figure 2. (D) Heat map of abundant bacterial species (average abundance >1%) among individuals between cases and controls. The relative abundance of bacterial species is represented by a color gradient as indicated. The species were ordered by decreasing relative abundance. (E) Species biomarkers identified by linear discriminative analysis (LDA) effect size (LEfSe) analysis between cases (in red) and controls (in green). LDA scores (log 10) for the enriched species in controls are represented on the positive scale, while LDA-negative scores indicate enriched species in cases. The threshold used to consider a discriminative feature for the LDA score was set at >2. Taxonomic biomarkers at higher levels are shown in Supplementary Figure 2.