Effect of maternal HIV status on the early neonatal microbiome

Microbiome disruption is a proposed mechanism for the observed differences in child health outcomes by maternal HIV status, but the early neonatal microbiome of HIV-exposed newborns is not well studied. We used 16S ribosomal ribonucleic acid sequencing to analyze microbiome compositions of nasal, skin, and rectal samples collected less than72 hours after birth from 57 hospitalized neonates in Botswana, 33% of whom were HIV-exposed. We observed no significant microbiome differences by maternal HIV status, except among a subgroup whose mothers had a recent HIV diagnosis, suggesting that any microbiome variations mediated by HIV exposure might only emerge later in infancy or may be reduced by HIV viral suppression and maternal immune reconstitution following antiretroviral therapy.