HIV infection cannot yet be cured, but antiretroviral therapy (ART) dramatically slows disease progression and reduces the risk of transmission to others, including reducing transmission from mother to child during pregnancy. However, children exposed to, but not infected by, HIV in this way have increased risk of childhood infections, slowed growth, and increased mortality. To better understand the mechanism at play, a recent study examined the gut microbiota of over 250 infant-mother pairs in Nigeria. In the first six months of life, the relative abundance of Bifidobacterium species was lower in HIV-exposed infants. Among HIV-exposed infants, breastfeeding was beneficial to their growth rate but did not correspond to a higher abundance of Bifidobacterium. In fact, the presence of ART drug metabolites in breastmilk was associated with reduced relative abundance of Bifidobacterium species. This reduction is important because Bifidobacterium species play key roles in the development of healthy infant gut microbiomes and immune systems. While the relationships that maternal HIV status and breastfeeding have with infant growth and microbiota development are complex, this study suggests that probiotic supplementation of Bifidobacterium may benefit these infants and that we need to further examine how ART drug metabolites in breastmilk impact infants.