Gut Microbiota Characterisation in HIV-Positive Adolescents and Young Adults in Côte d’Ivoire: A Shotgun Metagenomic Pilot Study with HIV-negative Controls

Abstract

Background: The gut microbiota may undergo alterations in people living with HIV, including those receiving antiretroviral therapy. However, data on adolescents and young adults living with HIV in West Africa remain limited. Objective: To characterise the gut microbiota of HIV-positive adolescents and young adults receiving antiretroviral therapy in Côte d’Ivoire and to compare it with that of HIV-negative controls. Methods: A cross-sectional, descriptive and comparative pilot study was conducted among 26 participants aged 10–24 years, comprising 13 HIV-positive participants and 13 HIV-negative controls. Faecal microbiota were analysed using shotgun metagenomics. Taxonomic composition, alpha diversity, beta diversity and the core microbiota were compared between groups. Alpha-diversity indices were compared using the Wilcoxon–Mann–Whitney test with Benjamini–Hochberg correction. Beta diversity was assessed using Bray–Curtis distances, principal coordinates analysis (PCoA), PERMANOVA and PERMDISP with 999 permutations. Results: Sequencing generated 294,656 reads, of which 252,522 were microbial reads (85.70%). The microbiota was mainly represented by Pseudomonadota (50.30%) and Bacillota (46.24%), while Bacteroidota accounted for 3.46%. Pseudomonadota showed similar proportions in HIV-positive and HIV-negative participants (50.89% vs 49.31%), whereas Bacteroidota was less represented in HIV-positive participants (1.14% vs 7.40%). No significant differences in alpha diversity were observed. Bray-Curtis PCoA showed substantial overlap between the groups; PERMANOVA did not identify a significant difference in overall community composition (pseudo-F = 0.419; R² = 0.017; p = 0.651), and PERMDISP showed no significant difference in dispersion (F = 1.064; p = 0.375). The core microbiota was largely shared between the groups. Faecalibacterium prausnitzii was more highly represented in HIV-negative controls (34.07% vs 0.73%), whereas Streptococcus salivarius, Stenotrophomonas maltophilia, Ochrobactrum anthropi and Achromobacter xylosoxidans were more highly represented in HIV-positive participants. Conclusion: HIV-positive and HIV-negative participants shared a substantial taxonomic core and did not differ significantly in overall microbial community structure, despite marked differences in the relative representation of several taxa. Given the pilot and exploratory nature of the study, the small sample size and the limited sequencing depth, these observations require confirmation in larger cohorts incorporating functional analyses and improved control of potential confounding factors and contamination.