Fig. 1

Low-microbial gene richness is linked to HIV-1-mediated immune suppression. a Probability density function showing a bimodal distribution of the study population according to gut microbial gene richness, i.e., the number of different microbial genes observed in each individual at 10 million sequence downsampling size. The local minimum between the two modes (621,808 genes in this analysis) was used as a threshold to define people with high (HGCs) and low-gene counts (LGCs). b The bimodal distribution became even more aparent when KEGG enzyme richness, i.e., number of different enzymes found in the KEGG database was used. c HIV-1-infected subjects (n = 156) were more likely to be classified as LGCs; in comparison, most HGCs were HIV-1 negative. d The association between LGC and HIV-1 infection remained when only men-who-have-sex-with-men (MSM) were analyzed (n = 100). e HIV-1 phenotypes associated with immune deterioration were enriched in LGCs. f Subjects with lower nadir CD4+ counts were gradually more likely to be classified as LGCs. Late presenter, subjects with CD4+ T-cell counts <200 cells/mm³ at diagnosis and no ART exposure; discordant, with HIV-1 RNA <50 copies/mL and CD4+ T-cell counts <300 cells/mm³; concordant, with HIV-1 RNA levels <50 copies/mL and achieving CD4+ T-cell counts >500 cells/mm³; early treated, HIV-1-infected subjects who initiated ART during the first 6 months after the infection, achieving HIV-1 RNA levels <50 copies/mL during at least 3 months and with no HIV-1 RNA blips after achieving HIV-1 RNA <50 copies/mL; ART naïve, with HIV-1 RNA >10,000 copies/mL, nadir CD4+ T-cell counts >500 cells/mm³ and no ART exposure; viremic controller, with HIV-1 RNA between 50 and 2000 copies/mL during at least 2 years in the absence of ART; elite controller, subjects with HIV-1 RNA <50 copies/mL during at least 2 years in the absence of ART