Analysis of the oral microbiome in individuals on pre-exposure prophylaxis (PrEP) for human immunodeficiency virus (HIV)

• Grant number: 24/23762-8
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: August 01, 2025
• End date: July 31, 2026
• Field of knowledge: Health Sciences - Dentistry - Dental Clinics
• Principal Investigator: Paulo Henrique Braz da Silva
• Grantee: Nilson Ferreira de Oliveira Neto
• Supervisor: Roger Junges
• Host Institution: Faculdade de Odontologia (FO). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: University of Oslo (UiO), Norway
• Associated to the scholarship: 23/14978-4 - Analysis of salivary biomarkers and the oral microbiome/virome of patients diagnosed with syphilis, BP.DR

Abstract

Saliva is a valuable biological fluid for identifying biomarkers, including microorganisms with potential infectivity. Its collection is accessible, rapid, and minimally invasive, making it an ideal medium for diagnostic studies. Pre-exposure prophylaxis (PrEP) for human immunodeficiency virus (HIV) involves the use of antiretroviral drugs to reduce the risk of infection. While previous studies have shown that oral PrEP can dysregulate the gut microbiome, its impact on the oral microbiome remains unexplored. As PrEP users often remain on prophylaxis long-term, understanding these changes is vital for informing policymakers and clinicians. This study aims to characterize the oral microbiome of PrEP users through 16S rRNA based profiling, focusing on the dynamics and genetic diversity of microbes in the oral cavity. Saliva samples were collected at the initial examination and during follow-up visits over a 12-month period, then stored at ¿80°C until analysis. Microbiome profiling will involve bacterial 16S rRNA sequencing, with raw data processed using DADA2 and Phyloseq pipelines. Data interpretation and visualization will be conducted with R packages and integrated tools such as Microbiome Analyst. Differential analyses, including microbiome composition and alpha and beta diversity comparisons, will be prioritized to reveal significant group differences.