Fig. 2

Lower microbial diversity and richness in controllers. Longitudinal a microbial gene richness at 10 million (10 M filtered reads) down-sampling size and b alpha diversity based on Shannon index in viremic controllers (gray) and non-controllers (white). c Principal coordinates analysis (PCoA) of microbial diversity based on Bray-Curtis distances at pre-vaccination and during ‘kick and kill’ intervention. Proportion of variance explained by each principal coordinate axis is reported in the corresponding axis label. Subjects per each group are represented by squares (controllers) and circles (non-controllers). Each point stands for one subject, color coded by group and time point. The increase in purple (controllers) and blue (non-controllers) colors reflects sequential time points from baseline (pre-Vax) to the second vaccine administration (MVA2). Ellipses delineate the distribution of points per each group. Gray arrows link directional changes in bacterial abundance throughout the kick and kill intervention from baseline (pre-Vax). PERMANOVA statistical analysis of samples grouped by group, PatientID (patient internal identifier), and time point is shown on the top of the panel. Abbreviations: MAP, monitored antiretroviral pause; pre-Vax, baseline (1 day before first MVA vaccination); MVA1, 1 week after first MVA vaccination; RMD, 1 week after third romidepsin infusion; MVA2, 4 weeks after second MVA vaccination. Unadjusted p values are shown. Benjamini–Hochberg multiple hypothesis correction for p values ≤ 0.05 are provided in Additional file 2: Dataset S7