Gut Microbiome Profiles and Associated Metabolic Pathways in HIV-Infected Treatment-Naïve Patients

• Main Authors: Wellinton M. do Nascimento, Aline Machiavelli, Luiz G. E. Ferreira, Luisa Cruz Silveira, Suwellen S. D. de Azevedo, Gonzalo Bello, Daniel P. Smith, Melissa P. Mezzari, Joseph F. Petrosino, Rubens Tadeu Delgado Duarte, Carlos R. Zárate-Bladés, Aguinaldo R. Pinto
• Format: Article
• Language: English
• Published: MDPI AG 2021-02-01
• Series: Cells
• Subjects: microbiome; human immunodeficiency virus; metabolism; virus subtypes; sexual orientation
• Online Access: https://www.mdpi.com/2073-4409/10/2/385

The normal composition of the intestinal microbiota is a key factor for maintaining healthy homeostasis, and accordingly, dysbiosis is well known to be present in HIV-1 patients. This article investigates the gut microbiota profile of antiretroviral therapy-naive HIV-1 patients and healthy donors living in Latin America in a cohort of 13 HIV positive patients (six elite controllers, EC, and seven non-controllers, NC) and nine healthy donors (HD). Microbiota compositions in stool samples were determined by sequencing the V3-V4 region of the bacterial 16S rRNA, and functional prediction was inferred using PICRUSt. Several taxa were enriched in EC compared to NC or HD groups, including <i>Acidaminococcus</i>, <i>Clostridium methylpentosum</i>, <i>Barnesiella</i>, <i>Eubacterium coprostanoligenes</i>, and <i>Lachnospiraceae UCG-004</i>. In addition, our data indicate that the route of infection is an important factor associated with changes in gut microbiome composition, and we extend these results by identifying several metabolic pathways associated with each route of infection. Importantly, we observed several bacterial taxa that might be associated with different viral subtypes, such as <i>Succinivibrio</i>, which were more abundant in patients infected by HIV subtype B, and <i>Streptococcus</i> enrichment in patients infected by subtype C. In conclusion, our data brings a significant contribution to the understanding of dysbiosis-associated changes in HIV infection and describes, for the first time, differences in microbiota composition according to HIV subtypes. These results warrant further confirmation in a larger cohort of patients.