Additional file 2: Dataset S1. Longitudinal microbial composition (relative abundance) in viremic controllers and non-controllers analyzed by MetaPhlAn2.0. Dataset S2. Raw bacterial protein counts at baseline in viremic controllers and non-controllers analysed using Scaffold Q+ software v4.9.0. Dataset S3. Raw gene counts at baseline in viremic controllers and non-controllers estimated using RSEM v1.3.0. Dataset S4. Soluble factors (normalized protein expression units) from the Olink inflammation panel at baseline in viremic controllers and non-controllers. Dataset S5. List of transcripts significantly correlated with the Bacteroidales:Clostridiales ratio adjusted for multiple comparisons (spearman’s rho and corresponding q-value<0.05 are reported). Dataset S6. Spearman’s correlation (rho=0.5) between viral reservoir (CA HIV-1 RNA and HIV-1 DNA), bacterial species (Bacteroidales and Clostrdiales), transcripts correlated with the ratio Bacteroidales / Clostridiales and differentially abundant microbial proteins (p<0.025). Dataset S7. Benjamini–Hochberg multiple hypothesis correction for unadjusted p-values ≤ 0.05 (metagenomics and metaproteomics datasets).