Fig. 1: Cohort characteristics.

A Timeline of samples analyzed from each individual. Non-shedder samples are shown as blue circles, shedder samples from concordant timepoints are shown as red circles, and shedder samples from discordant shedding timepoints are shown as black triangles. ART antiretroviral therapy. B Samples grouped by microbiome community cluster. Samples are shown as vertical bars colored by species relative abundance. Metadata is shown as rows of colored squares beneath the samples. By multinomial logistic regression, community clusters were not associated with ART duration or shedder/non-shedder status, except for cluster 3, which was associated with non-shedder status (two-sided, adjusted p-values in Supplementary Data 3). Cluster 3 consists of two samples from the same non-shedder individual.