Effects of HAART and Time on the Beta Diversity of Breast Milk Microbiome in HIV-infected Postpartum Women

Abstract

Introduction - Highly active antiretroviral therapy (HAART) has been used in HIV-infected pregnant women to suppress viral replication and reduce perinatal transmission. However, the influence of HAART on the breast milk microbiome remains largely unknown. In addition, analysis of unbalanced longitudinal studies of β-diversity data is limited by a lack of appropriate statistical methods. The purpose of this study is to investigate the effects of HAART and time on β-diversity of breast milk microbiome from HIV-infected women during the first month postpartum using a novel statistical analysis method. Methods - HIV-infected pregnant women in Nairobi, Kenya in two separate studies were randomized to receive either HAART (treated group) during pregnancy to 6 months postpartum or short course zidovudine (control group) up to delivery. Breast milk samples were collected from 25 treated and 24 control women every week during the first month postpartum. These samples were subjected to 16S ribosomal sequencing. Microbial community analysis (PERMANOVA with restricted permutation for β-diversity) was used to determine the effects of HAART and time on the breast milk microbiome. Results - PERMANOVA analysis revealed statistically significant changes in breast milk microbiome β-diversity when comparing postpartum week 1 to week 4 (p < 0.01). In contrast, no obvious difference was detected between the treated and control groups. Conclusion - PERMANOVA analysis with restricted permutation was used to evaluate the effects of time and treatment in mixed models on an unbalanced longitudinal dataset. During the first month postpartum, the β-diversity of the breast milk microbiome changed significantly in HIV-infected women from both arms of the trials. In contrast, HAART treatment had minimal effects on the β-diversity.