Expanded Enteric Virome and Altered Bacterial Microbiome in Acquired Immunodeficiency Syndrome. Expanded Virome in AIDS

The effect of HIV on the enteric DNA virome and bacterial microbiome is incompletely characterized. Here we sequenced virus-like particles and bacterial 16S ribosomal RNA genes in stool from 40 HIV-negative subjects, 42 HIV-infected subjects and 40 HIV-infected subjects on anti-retroviral therapy (ART) living in Uganda. CD4 T cell counts inversely correlated with plasma soluble CD14 (sCD14) levels, suggesting increased translocation of pro-inflammatory microbial products across the enteric mucosa with worsening immunodeficiency. Low CD4 T cell counts were associated with expansion of the eukaryotic DNA virome including adenoviruses and Anelloviruses and changes in the bacterial microbiome including increases in Enterobacteriaceae members and decreases in Ruminococci. Thus immunodeficiency in progressive HIV infection is associated with significant alterations in the human enteric virome and bacterial microbiome. These changes may contribute to acquired immunodeficiency syndrome (AIDS) enteropathy, translocation of pro-inflammatory materials across the intestinal mucosa and systemic inflammation associated with progression to AIDS.