Figure 1

Schematic of sampling and bioinformatic methodology. Rectal mucosa secretions were collected from 60 human subjects as shown and subjected to high-throughput deep V4 16S sequencing. Alpha and beta diversity analyses were then performed, which suggested microbial composition was altered in HIV-infected subjects who were not receiving combination anti-retroviral therapy (cART). Microbial differences in these subjects were identified and compared with HIV-infected subjects receiving cART. In addition, the different classes of cART were analyzed to determine whether any class was significantly associated with differences in microbial composition. Imputed metagenomic differences between HIV-infected subjects not receiving cART and healthy control subjects were then identified and compared between the three patient cohorts. PICRUSt, phylotypic investigation of communities by reconstruction of unobserved states; HUMAnN, HMP unified metabolic analysis network.