Uncovering the role of gut microbiota in HIV acquisition and vaccine response in infant monkeys

The HIV/AIDS epidemic remains one of the world’s most critical public health problems. Following decades of research on HIV pathogenesis, there is a growing wealth of studies that have characterized the dysbiosis of gut microbiota caused by HIV in infected patients. Inversely, however, it is still unclear whether these diverse communities of microorganisms, which play a fundamental role in host physiology, affect susceptibility to HIV infection. Here, we analyzed 16S rRNA gene sequencing data from fecal samples of infant rhesus macaques in a pediatric HIV vaccine study, which includes HIV and control vaccine groups (immunized at 0, 6, and 12 weeks of age; n=12/group). Starting at 15 weeks of age, all monkeys were orally challenged with SHIV every week until they became infected. Although the HIV vaccine did not confer protection, the animals exhibited variable time to acquisition of SHIV. We compared the overall microbial profile of animals from the two groups and found that the HIV vaccine caused changes in the gut microbiota despite its failure to provide protection. Additionally, we identified 7 bacterial taxa that were bioinformatically associated with increased susceptibility of HIV, and 2 taxa that were associated with decreased susceptibility. Importantly, one of the protective taxa, Lactobacillus gasseri, has previously been experimentally confirmed as inhibiting HIV infection of human tissue in vitro, which helps validate our overall findings. Taken together, our results support the idea that the gut microbiota impacts acquisition of HIV and provides new insights on its prevention.