Fig. 2: Bacteriome in shedders and non-shedders.

A Bacterial species Bray–Curtis dissimilarity between pairs of samples from the same individual (within-individual comparisons; n = 134 pairwise comparisons for non-shedder samples and n = 58 pairwise comparisons for shedder samples) or from different individuals (between-individual comparisons; n = 3694 pairwise comparisons for non-shedder samples and n = 608 pairwise comparisons for shedder samples). In this and panel B, statistical significance was assessed using a two-sided, two-sample permutation test, and p-values were adjusted for multiple comparisons using the Benjamini–Hochberg method. In this and B, D, center lines show the median, box bounds show the interquartile range, and whiskers show the minimum and maximum. B Bacterial species Bray–Curtis dissimilarity between pairs of concordant samples within the same shedder individual, or sample pairs where one sample was from a discordant shedding timepoint and the other was from a concordant timepoint within the same individual. The corresponding timepoints from matched non-shedder individuals serve as a control. C PCoA of shedder and non-shedder samples, using Bray–Curtis dissimilarity calculated from bacterial species relative abundance. Samples are colored by duration of ART (antiretroviral therapy). Non-shedder samples are shown as circles, and shedder samples are shown as triangles. Statistical significance was determined by PERMANOVA, p = 0.33 for ART duration and p = 0.34 for shedder/non-shedder status. D Mycoplasma hominis relative abundance in non-shedders and shedders. Statistical significance was determined by MaAsLin2, adjusted two-sided p-value = 0.048. E PCoA of shedder samples, using Bray–Curtis dissimilarity calculated from bacterial species relative abundance. Discordant shedding timepoints are colored brown, and concordant timepoints are colored green. Statistical significance was determined by PERMANOVA, p = 0.85.