New insights into the breast milk virome in women with HIV

From the Human Biology Division

Breast milk (BM) contains bacterial and viral communities that colonize the infant's gut, add microbial diversity, and shape the gut microbiome early in life. A growing number of studies suggests that the bacterial microbiome established early in life might have long-term health consequences, and thus alterations in the BM microbiome are likely to impact infant health. In collaboration with researchers from the Center of Fundamental and Applied Microbiomics at the Biodesign Institute at Arizona State University, the Lehman lab in the Human Biology Division sought to investigate if the BM bacterial microbiome and virome (community of viruses) composition is affected by severe immunosuppression in a cohort of Kenyan women living with HIV (WLHIV) and determine if BM virome diversity can be associated with mortality in HIV-infected infants. Their results are now published in the journal mSystems from the American Society for Microbiology.

Overview of study design.
Overview of study design Image from publication.

HIV infection is known to alter the enteric microbiome, however, little is known about the effects of immunosuppression due to HIV infection in the BM bacterial microbiome and virome. To compare the bacterial microbiome and virome diversity between women with high and low CD4 counts –an indicator of the degree of immune function– Maqsood and colleagues sequenced the bacterial microbiome and the DNA virome on BM samples collected from a cohort of Kenyan women at one month postpartum. Of note, at the time of the study (1990-2002), the standard of care did not include combination antiretroviral therapy (cART). Importantly, the BM samples used here are over 20 years old and due to instability of RNA and limited sample volumes, the study only assessed the DNA virome.

The group found very similar bacterial taxa in both CD4 high and low groups. In the virome, cytomegalovirus (CMV) dominated the samples in both groups, and no discriminant viruses were found. Dr. Dara Lehman, one of the principal investigators in the study, added: "This is the first study of virome in breast milk in women living with HIV. We show that immunosuppression does not significantly alter the virome or the bacterial microbiome in breastmilk in this Kenyan cohort."

Next, the researchers evaluated whether the breast milk DNA virome might be associated with infant mortality. The samples in both groups were dominated by CMV, and there was no difference in average relative abundance between women whose infants lived versus died. Similarly, there was no significant difference in virome species richness between infant mortality groups, a metric known as alpha diversity. When the researchers compared beta diversity or the differences in viral communities between groups, they found higher beta diversity in the mothers of infants that died. Further analysis revealed that anelloviruses, a ubiquitous group of viruses in humans, might be driving the differences between groups, but qPCR analysis demonstrated that anellovirus levels were not significantly different in BM between infant outcome groups.

Dr. Lehman explained the limitations of the study and discussed future directions: "This study was limited to archived samples collected from women with HIV infection in Kenya at a time before antiretroviral therapy (ART) was widely available.  We did not have samples from HIV-infected women on ART or from uninfected women to compare to the results we present here. We are interested in determining whether breastmilk microbiota differ in HIV-infected women on ART or HIV-uninfected women. Currently, we are following a new cohort of mother-baby pairs in Kenya in which we are collecting breastmilk, stool and blood from the mothers and also stool and blood from their infants. Half of the women in this new study are HIV-infected and half are HIV-uninfected, and this will provide us the opportunity to determine whether HIV status of the mom impacts virome acquisition of the infants. Because other studies show that infant morbidity and mortality is higher in HIV-exposed uninfected infants compared to HIV-unexposed infants, we hypothesize that this is in part due to acquisition of an altered virome/bacterial microbiome due to the HIV status of the mom."

Maqsood, R, Reus, JB, Wu, LI, Holland, LA, Nduati, R, Mbori-Ngacha, D, Maleche-Obimbo, E, Begnel, ER, Gantt, S, Ojee, E, Wamalwa, D, John-Stewart, G, Slyker, J, Lehman, DA, & Lim, ES. (2021). Breast Milk Virome and Bacterial Microbiome Resilience in Kenyan Women Living with HIV. mSystems6(2), e01079-20.

This work was supported by grants from the National Institutes of Health.