Evolution of the gut microbiome following acute HIV-1 infection

Muntsa Rocafort, Marc Noguera-Julian, Javier Rivera, Lucía Pastor, Yolanda Guillén, Jost Langhorst, Mariona Parera, Inacio Mandomando, Jorge Carrillo, Víctor Urrea, Cristina Rodríguez, Maria Casadellà, Maria Luz Calle, Bonaventura Clotet, Julià Blanco, Denise Naniche, Roger Paredes

Research output: Contribution to journalArticleResearch

47 Citations (Scopus)


© 2019 The Author(s). Background: In rhesus macaques, simian immunodeficiency virus infection is followed by expansion of enteric viruses but has a limited impact on the gut bacteriome. To understand the longitudinal effects of HIV-1 infection on the human gut microbiota, we prospectively followed 49 Mozambican subjects diagnosed with recent HIV-1 infection (RHI) and 54 HIV-1-negative controls for 9-18 months and compared them with 98 chronically HIV-1-infected subjects treated with antiretrovirals (n = 27) or not (n = 71). Results: We show that RHI is followed by increased fecal adenovirus shedding, which persists during chronic HIV-1 infection and does not resolve with ART. Recent HIV-1 infection is also followed by transient non-HIV-specific changes in the gut bacterial richness and composition. Despite early resilience to change, an HIV-1-specific signature in the gut bacteriome - featuring depletion of Akkermansia, Anaerovibrio, Bifidobacterium, and Clostridium - previously associated with chronic inflammation, CD8+ T cell anergy, and metabolic disorders, can be eventually identified in chronically HIV-1-infected subjects. Conclusions: Recent HIV-1 infection is associated with increased fecal shedding of eukaryotic viruses, transient loss of bacterial taxonomic richness, and long-term reductions in microbial gene richness. An HIV-1-associated microbiome signature only becomes evident in chronically HIV-1-infected subjects.
Original languageEnglish
Article number73
Publication statusPublished - 11 May 2019


  • AIDS
  • HIV-1
  • HIV-1 pathogenesis
  • Microbiome
  • acute HIV-1 infection


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