bbeckley-hub/Vaginal-Microbiome-Study-Nigeria

Impact of Antiretroviral Treatment on Vaginal Microbiome Composition in People Living with HIV # Vaginal Microbiome Study – Nigeria **Impact of Antiretroviral Treatment on Vaginal Microbiome Composition in People Living with HIV** This repository contains the complete R analysis pipeline and supplementary data for the manuscript: > *"Impact of Antiretroviral Treatment on Vaginal Microbiome Composition in People Living with HIV"* > Authors: Adesola Olalekan, Brown Beckley, Ogunsanya Oluwabunmi, Felix Agomma, Olarenwaju Ademuyiwa > Affiliation: University of Lagos, Nigeria; University of Ghana; KNUST, Ghana; Onikan General Hospital, Lagos. ## Project Overview We used PacBio long‑read 16S rRNA sequencing to characterise the vaginal microbiome of five women in Lagos, Nigeria – three HIV‑positive (two with a one‑month follow‑up after ART initiation, one with only a baseline) and two HIV‑negative controls – yielding seven samples. Our objectives were to compare microbiome composition by age, *Lactobacillus* diversity, pathogen prevalence, strain consistency, and the effect of ART, and to identify potentially novel bacterial taxa. All raw sequencing reads are deposited in the NCBI Sequence Read Archive under accession **PRJEB124225**. ## Repository Structure ``` Vaginal-Microbiome-Study-Nigeria/ ├── Rscripts/ # All R analysis scripts (numbered in order) │ ├── 01_dada2_preprocessing.R # DADA2: from FASTQ to ASV table and taxonomy │ ├── 02_phyloseq_setup.R # Create phyloseq object │ ├── 03_alpha_beta_diversity.R # Alpha & beta diversity, PCoA, PERMANOVA │ ├── 04_genus_composition.R # Genus bar plots and heatmap (Figure 1A, 1B, S1) │ ├── 05_lactobacillus_analysis.R # Lactobacillus ASVs, BLAST species assignment │ ├── 06_pathogen_analysis.R # Pathogen prevalence (Figure 3, Table 1) │ ├── 07_differential_abundance.R # DESeq2 differential abundance (Figure 4, Table S4) │ ├── 08_jaccard_analysis.R # Jaccard distances (Table S5) │ ├── 09_novel_microbe_detection.R …