16S rRNA Gene-Amplicon-Based Profiling of the Vaginal Microbiome From North African Women

The vaginal microbiome is designed to have low bacterial diversity and is dominated by Lactobacillus species, which acidify this environment and protect against invading pathogens. However, dysbiosis of the vaginal microbiome contributes to many pathologies, including bacterial vaginosis (BV). In microbiome research, NGS technologies are used to analyze the 16S rRNA gene, a molecular marker present in all bacteria and archaea. This gene variability allows researchers to identify different microbial species, providing insights into community composition and diversity. We explored the vaginal microbiome composition in thirty-three North African women using 16S rRNA V3–V4 region sequencing. The number of samples was 11 diseased non-pregnant (DNP), 7 diseased pregnant (DP), 9 healthy non-pregnant (HNP), and 6 healthy pregnant (HP) women at reproductive age (25–40 years old). We intended to identify bacterial taxonomy and diversity using two bioinformatics tools, the DADA2 and EzBioCloud 16S-based Microbiome Taxonomic Profiling (MTP) pipelines. Our findings revealed an overrepresentation of pathogenic bacteria at the species level within women with BV, identified using the EzBioCloud MTP pipeline. Consequently, our efforts resulted in the effective elucidation of bacterial species and diversity using the EzBioCloud 16S-based MTP pipeline. This result contrasts with our efforts using DADA2, where the objective of species differentiation remained unachievable. EzBioCloud makes it a feasible choice for incorporation into clinical diagnostic protocols and novel therapy techniques for bacterial vaginosis. Its ability to distinguish microbiome taxonomy and identify constituent species has the potential to improve our understanding of this disorder and potentially guide therapeutic interventions.