Handley et al. demonstrate that vaccination against SIV infection in Rhesus macaques prevents alterations in the gastrointestinal virome and bacterial microbiome that are typically associated with poor disease outcome.. SIV Vaccination Metagenome

Pathogenic simian immunodeficiency virus (SIV) infection is associated with AIDS, expansion of the eukaryotic enteric virome, consequent intestinal epithelial damage, translocation of viral and bacterial components into the circulation and systemic immune activation. Here we characterized changes in the enteric virome and bacterial microbiome during pathogenic SIV infection, and determined whether vaccine-mediated protection altered these disease manifestations. Vaccine-associated protection against SIV infection prevented expansion of the enteric virome. Overall gastrointestinal bacterial community structure was indistinguishable in protected and unprotected animals, however, animals that ultimately succumb to AIDS related disease had altered levels of several bacterial taxa including an increased abundance of many disease-associated bacteria. These data suggest that immune control of SIV-induced immunodeficiency aids in the maintenance of a normal fecal microbiome and ameliorates SIV-associated systemic inflammation.