dominant lactobacillus spp  (Cell Signaling Technology Inc)

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

Journal: PLOS Computational Biology

Article Title: Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy

doi: 10.1371/journal.pcbi.1011295

Figure Lengend Snippet: (A) Model schematic of a generalized Lotka-Volterra Model for three community groups: optimal Lactobacillus spp. (oLB), L . iners (Li), and non-optimal anaerobic bacteria (nAB). Model equations capture growth rates, carrying capacity and interaction terms. (B) Parameter ranges used to define uniform distributions for a global uncertainty and sensitivity analysis using Latin Hypercube Sampling (LHS). (C) Mapping of the model predicted steady-state compositions to model defined CSTs using a nearest centroid model based on VALENCIA centroids. (D) Analysis of the overall frequency of multi-stable states from the model predicted versus clinical observations in two cohorts (HMP and Gajer cohorts). Statistical comparisons were made using χ2-tests. (E) Equilibrium frequencies from the base model parameter space predicted and clinical frequencies of the HMP Cohort (N = 101, pink) and the Gajer Cohort (N = 32, teal). Statistical comparisons were made using χ2-tests. P-values were represented as n.s. (not significant, P > 0.05), * (P < 0.05), ** (P < 0.01), *** (P < 0.001), **** (P < 0.0001) and were not adjusted for multiple comparisons.

Article Snippet: The simplified CSTs included the “optimal” Lactobacillus spp.- dominated state (oLB dominated, combined CST -I, -II, -V), the Lactobacillus sp., L . iners- dominated state (Li dominated, CST -III), and a state with high bacterial diversity, associated with non-optimal anaerobic bacteria (nAB) and BV (nAB dominated, CST -IV; ).

Techniques: Bacteria, Sampling

Journal: PLOS Computational Biology

Article Title: Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy

doi: 10.1371/journal.pcbi.1011295

Figure Lengend Snippet: The analysis was stratified dependent on the Lactobacillus spp. that was dominant pre-menses (A-D) are associated with oLB dominated equilibrium behavior (1SS oLB dominated and 2SS oLB dominated/nAB dominated) and (E-H) are associated with Li dominated equilibrium behavior (1SS Li dominated and 2SS Li dominated/nAB dominated subtypes). (A) Mean and ± 95% confidence interval of model predicted composition before, during (red), and after menses for nAB, Li, and oLB relative abundance. Data are plotted in aggregate (all data) and stratified by composition on the last day of menses. Samples that were nAB became dominant by the last day of menses were considered sensitive (middle) and those that remained Lactobacillus spp. dominant were considered resilient (right). (B) Mean and ± 95% confidence interval of nAB, Li, and oLB relative abundance for the HMP cohort data five days before menses, four representative time points during menses, and five days after menses. Data are plotted by aggregate and response types as described in panel A. (C) Volcano plot comparing parameter differences between the sensitive (blue) and resilient (gold) response types from the model simulation. (D) Comparison of clinical versus model predictions for the frequency of menses-sensitive samples. (E-H) Corresponding analysis for the Li dominated states (E) Model simulations in aggregate and stratified by response type (F) Clinical observations in aggregate and stratified by response type. (G) Volcano plot of parameters that differ between response types. (H) Comparison of clinical versus model predictions for the frequency of menses-sensitive samples. Statistical comparisons of frequency were made using χ2-tests. The magnitude of menses perturbation in this figure was -200% k grow-oLB /kgrow-Li and +100% α oLB→nAB /α oLi→nAB .

Article Snippet: The simplified CSTs included the “optimal” Lactobacillus spp.- dominated state (oLB dominated, combined CST -I, -II, -V), the Lactobacillus sp., L . iners- dominated state (Li dominated, CST -III), and a state with high bacterial diversity, associated with non-optimal anaerobic bacteria (nAB) and BV (nAB dominated, CST -IV; ).

Techniques: Comparison

Journal: Journal of Clinical Medicine

Article Title: Identification of Vaginal Microbial Communities Associated with Extreme Cervical Shortening in Pregnant Women

doi: 10.3390/jcm9113621

Figure Lengend Snippet: Association of CSTs and cervical shortening categorization.

Article Snippet: other Lactobacillus spp.-dominated community (CST I, CST II, CST V) , 3 (30.0%) , 22 (73.3%).

Techniques: