Composition of gut microbiota of children and adolescents with perinatal HIV infection taking antiretroviral therapy in Zimbabwe

Background HIV infection causes impairment of the gastrointestinal barrier, with substantial depletion of CD4+ T-cells in the gut. Antiretroviral therapy (ART) restores CD4+ counts and may have beneficial effects on gut microbiota in adults. Little is known about effect of long-term ART on gut microbiome in HIV infected children. We investigated composition of gut microbiota in HIV infected and uninfected children and assessed associations between gut microbiota and patient characteristics. Methods In a cross-sectional study, rectal swabs were collected from 177 HIV infected and 103 HIV uninfected controls. Gut microbial composition was explored using 16S rRNA sequencing (Illumina Miseq). Results HIV infected children had significantly lower alpha-diversity and higher beta-diversity compared to HIV uninfected. No association was observed between microbiome diversity and CD4+ T-cell count, HIV viral load or HIV-associated chronic lung disease. We found enriched levels of Corynebacterium (p<0.01), Finegoldia (p<0.01) and Anaerococcus (p<0.01) in HIV infected, and enrichment of Enterobacteriaceae (p=0.02) in participants with low CD4+ counts (<400 cells/mm3). Prolonged ART-treatment (≥10 years) was significantly associated with a richer gut microbiota by alpha diversity. Conclusion HIV infected children have altered gut microbiota. Prolonged ART may restore the richness of the microbiota closer to that of HIV-uninfected children.