Breast milk virome and bacterial microbiome resilience in kenyan women living with hiv

Rabia Maqsood, Joshua B. Reus, Lily I. Wu, La Rinda A. Holland, Ruth Nduati, Dorothy Mbori-Ngacha, Elizabeth Maleche-Obimbo, Emily R. Begnel, Soren Gantt, Ednah Ojee, Dalton Wamalwa, Grace John-Stewart, Jennifer Slyker, Dara A. Lehman, Efrem S. Lim

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Breast milk is nutritionally and immunologically beneficial in early life but is also a potential source of infection. Little is known about breast milk microbiota of women living with HIV (WLHIV), the impact of severe immunosuppression, and the contribution to mortality of HIV-exposed infants. Here, we performed metagenomic sequencing to characterize the bacterial microbiome and DNA virome of breast milk samples at 1month postpartum from Kenyan WLHIV who were not receiving combination antiretroviral therapy (cART), 23 women with CD4 counts of ,250 and 30 women with CD4 of .500; and additionally, 19 WLHIV with infants that lived and 26 WLHIV with infants that died during the first 2 years of life were included. We found that breast milk bacterial microbiomes in this study population were highly diverse but shared a core community composed of the Streptococcaceae, Staphylococcaceae, Moraxellaceae, and Eubacteriaceae families. The breast milk virome was dominated by human cytomegalovirus (CMV) and included the bacteriophage families Myoviridae, Siphoviridae, and Podoviridae. Bacterial microbiome and virome profiles and diversity were not significantly altered by HIV immunosuppression, as defined by a CD4 of ,250. CMV viral load was not associated with maternal CD4 counts or infant mortality. In conclusion, we show that the core bacterial and viral communities are resilient in breast milk despite immunosuppression in WLHIV.

Original languageEnglish (US)
Article numbere01079-20
Issue number2
StatePublished - Mar 2021


  • Breast milk
  • CMV
  • HIV
  • Microbiome
  • Virome

ASJC Scopus subject areas

  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Physiology
  • Biochemistry
  • Computer Science Applications
  • Microbiology
  • Modeling and Simulation


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