Evolution of the gut microbiome following acute HIV-1 infection

• Published in: Microbiome Vol. 7; no. 1; pp. 73 - 17
• Main Authors: Rocafort, Muntsa, Noguera-Julian, Marc, Rivera, Javier, Pastor, Lucía, Guillén, Yolanda, Langhorst, Jost, Parera, Mariona, Mandomando, Inacio, Carrillo, Jorge, Urrea, Víctor, Rodríguez, Cristina, Casadellà, Maria, Calle, Maria Luz, Clotet, Bonaventura, Blanco, Julià, Naniche, Denise, Paredes, Roger
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 11.05.2019; BioMed Central; BMC
• Subjects: Acute Disease; acute HIV-1 infection; Adenoviruses; Adult; AIDS; Anergy; Antiretroviral agents; Antiretroviral therapy; Antiviral agents; Bacteria - classification; Bacteria - isolation & purification; Bioinformatics; CD4-Positive T-Lymphocytes; CD8 antigen; CD8-Positive T-Lymphocytes; Chronic Disease; Chronic infection; Digestive system; Feces - virology; Female; Gastrointestinal Microbiome; Genes; Genomes; Gut microbiota; HIV; HIV infections; HIV Infections - drug therapy; HIV Infections - microbiology; HIV-1; HIV-1 - isolation & purification; HIV-1 pathogenesis; Human immunodeficiency virus; Humans; Infeccions per VIH; Infections; Inflammation; Intestinal microflora; Lymphocytes; Lymphocytes T; Male; Metabolic disorders; Metagenomics; Microbiome; Microbiomes; Microbiota; Microbiota (Symbiotic organisms); Middle Aged; Monkeys & apes; Mozambique; Prospective Studies; Risk factors; Simian immunodeficiency virus; Studies; T cells; Taxonomy; Transcriptome; Type 2 diabetes; Viral Load; Virus diseases; Virus Shedding; Viruses; Young Adult; Mozambique; HIV-1; AIDS; HIV-1 pathogenesis; acute HIV-1 infection; Microbiome
• ISSN: 2049-2618; 2049-2618
• DOI: 10.1186/s40168-019-0687-5

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). 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. 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.