Journal: International Journal of Molecular Sciences

Article Title: Cervicovaginal Microbiome and HPV: A Standardized Approach to 16S/ITS NGS and Microbial Community Profiling for Viral Association

doi: 10.3390/ijms26168090

Figure Lengend Snippet: Cervicovaginal microbiome profiles of 66 cytology samples. ( A ). The dot plot shows Lactobacillus abundance per sample. Clustering identified three Lactobacillus states: L. -dominant (CST I–III, V), L. -diminished (IV-A), and L. -depleted (IV-B) based on abundance levels. Mean values with 95% CI and red reference lines distinguish these states. ( B ). The stacked bar chart shows microbial composition (%) per sample, based on the proportion of mapped reads. Of 30 species identified by 16S sequencing, the top 17 are shown in the legend. For each sample, the V-region with the best species-level resolution is displayed. ( C ) The merged stacked bar chart shows microbial composition by CST, highlighting the dominant species within each group. ( D ) The Venn diagram compares species abundance across CST, using CST I as the reference. Unique species (n) in CST II–V appear in the arms of the diagram, with those showing an absolute fold change > 1.5 noted in parentheses. ( E ) The bar chart highlights the significant shift in species (n = 27) for CST IV-B compared to CST I, marked by an enrichment of facultative and/or anaerobic organisms (green bars) and depletion of L. crispatus , gasseri , and jensenii (gray bars).

Article Snippet: For all the L. -diminished (CST IV-A) and L. -depleted (CST IV-B) samples, the dominant Lactobacillus spp. was L. iners , while the dominant opportunistic pathogen was G. vaginalis .

Techniques: Sequencing

Journal: International Journal of Molecular Sciences

Article Title: Cervicovaginal Microbiome and HPV: A Standardized Approach to 16S/ITS NGS and Microbial Community Profiling for Viral Association

doi: 10.3390/ijms26168090

Figure Lengend Snippet: Alignment of reads classified as “ Lactobacillus spp. unknown” to L. paragasseri and L. gasseri 16S rRNA genes. ( A ) Representative L. gasseri and L. paragasseri genomes show multiple 16S loci, with ambiguous reads mapping to expected locations. ( B ) In four samples containing ambiguous Lactobacillus spp. reads (30856-007; 30663-013, -034, -040), the V1V2 and V5V7 consensus sequences matched L. paragasseri (NR179257), distinguished from L. gasseri (NR975051) by SNPs at positions 101 (G/A) and 1052 (T/A), marked by red arrows.

Article Snippet: For all the L. -diminished (CST IV-A) and L. -depleted (CST IV-B) samples, the dominant Lactobacillus spp. was L. iners , while the dominant opportunistic pathogen was G. vaginalis .

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Cervicovaginal Microbiome and HPV: A Standardized Approach to 16S/ITS NGS and Microbial Community Profiling for Viral Association

doi: 10.3390/ijms26168090

Figure Lengend Snippet: Diversity analysis of microbial species in liquid cytology samples by Community State Types (CST). ( A ) Simpson and Shannon rarefaction curves plateaued at 28,000 reads, indicating sufficient sampling depth across all 66 samples. ( B ) Boxplots summarize CST-grouped samples. Colored points represent individual samples. Species richness (Simpson’s index) and evenness (Shannon entropy) significantly increased from Lactobacillus -dominant (CST I–III, V) to L. -diminished and L. -depleted states (CST IV-A, IV-B). MWU: Mann–Whitney U test. ns, not significant.

Article Snippet: For all the L. -diminished (CST IV-A) and L. -depleted (CST IV-B) samples, the dominant Lactobacillus spp. was L. iners , while the dominant opportunistic pathogen was G. vaginalis .

Techniques: Sampling, MANN-WHITNEY

Journal: International Journal of Molecular Sciences

Article Title: Cervicovaginal Microbiome and HPV: A Standardized Approach to 16S/ITS NGS and Microbial Community Profiling for Viral Association

doi: 10.3390/ijms26168090

Figure Lengend Snippet: Clustered Heatmap of Microbial Abundance in Liquid Cytology Samples. ( A ) Two-way hierarchical clustering of 66 samples and microbial species reveals distinct CST patterns. L. iners formed the earliest clusters, with a shift toward a diverse, anaerobic community in CST IV-B. Lactobacillus species (blue overlay) cluster with CST I–III and V, while anaerobes (pink overlay) associate with CST IV-A and IV-B. Differences in species abundance are quantified using Pearson’s distance metric. ( B ) Aggregated heatmaps grouped by CST, HPV type/status and Pap smear diagnosis highlight distinct microbial signatures. Notably, the seven most abundant anaerobic pathogens (pink overlay) in CST IV-B (rectangular outline) are also enriched in HPV-16 positive and HSIL samples.

Article Snippet: For all the L. -diminished (CST IV-A) and L. -depleted (CST IV-B) samples, the dominant Lactobacillus spp. was L. iners , while the dominant opportunistic pathogen was G. vaginalis .

Techniques: Biomarker Discovery

Journal: International Journal of Molecular Sciences

Article Title: Cervicovaginal Microbiome and HPV: A Standardized Approach to 16S/ITS NGS and Microbial Community Profiling for Viral Association

doi: 10.3390/ijms26168090

Figure Lengend Snippet: CLC Workflows, Tools, and Databases. ( A ) The Microbial Genomics Module offers workflows (blue arrow) and tools (black arrow) for taxonomic and diversity analysis ( left ), alongside the databases and dataset used in this study ( right ). ( B ) The Data QC and Taxonomic Profiling workflow uses the customized VAGIBIOTA or UNITE Reference Index (red outline) to generate QC reports and Abundance Tables from NGS reads obtained from clinical samples. These tables feed into the diversity analysis workflow. ( C ) Reads identified as “ Lactobacillus spp. unknown” are further analyzed using the Map Reads to Reference workflow which incorporates the VAGIBIOTA Sequence List for species identification ( left ). The Merge and Estimate Alpha and Beta Diversities workflow produces diversity plots and statistics ( right ).

Article Snippet: For all the L. -diminished (CST IV-A) and L. -depleted (CST IV-B) samples, the dominant Lactobacillus spp. was L. iners , while the dominant opportunistic pathogen was G. vaginalis .

Techniques: Sequencing