Diversity of vaginal microbiome and metabolome during genital infections
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Ceccarani C, Foschi C, Parolin C, D'Antuono A, Gaspari V, Consolandi C, Laghi L, Camboni T, Vitali B, Severgnini M, Marangoni A
Journal
Scientific reports
Year
2019
We characterized the vaginal ecosystem during common infections of the female genital tract, as vulvovaginal candidiasis (VVC, n = 18) and Chlamydia trachomatis infection (CT, n = 20), recruiting healthy (HC, n = 21) and bacterial vaginosis-affected (BV, n = 20) women as references of eubiosis and dysbiosis. The profiles of the vaginal microbiome and metabolome were studied in 79 reproductive-aged women, by means of next generation sequencing and proton based-nuclear magnetic resonance spectroscopy. Lactobacillus genus was profoundly depleted in all the genital infections herein considered, and species-level analysis revealed that healthy vaginal microbiome was dominated by L. crispatus. In the shift from HC to CT, VVC, and BV, L. crispatus was progressively replaced by L. iners. CT infection and VVC, as well as BV condition, were mainly characterised by anaerobe genera, e.g. Gardnerella, Prevotella, Megasphaera, Roseburia and Atopobium. The changes in the bacterial communities occurring during the genital infections resulted in significant alterations in the vaginal metabolites composition, being the decrease of lactate a common marker of all the pathological conditions. In conclusion, according to the taxonomic and metabolomics analysis, we found that each of the four conditions is characterized by a peculiar vaginal microbiome/metabolome fingerprint.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
Subjects
- Location of subjects
- Italy
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Chlamydia trachomatis infectious disease chlamydia,Chlamydia Infections,Chlamydia trachomatis caused disease or disorder,Chlamydia trachomatis disease or disorder,Chlamydia trachomatis infectious disease,chlamydia trachomatis infectious disease,chlamydial disease,Chlamydial Infection,Chlamydial infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chlamydia trachomatis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ‘Chlamydia’ (CT) (detection of C. trachomatis DNA by Versant CT/GC DNA 1.0 Assay)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- n/a
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Kruskall-Wallis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
Source: Table 2
Description: Differential microbial abundance between controls and chlamydia subjects
Abundance in Group 1: increased abundance in Chlamydia trachomatis
Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Vulvovaginal candidiasis Candidal vulvovaginitis,candidal vulvovaginitis,Candidal vulvovaginitis (disorder),Candidal vulvovaginitis NOS (disorder),Candidal: [vulvovaginitis NOS] or [cervix],candidal: [vulvovaginitis NOS] or [cervix],candidal: cervix,Candidiasis of vulva and vagina,candidiasis of vulva and vagina,Candidiasis, Vulvovaginal,Monilial vulvovaginitis,monilial vulvovaginitis,vaginal candidiasis,Vulvovaginal Candidiasis,vulvovaginal candidiasis,Vulvovaginal candidiasis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vulvovaginal candidiasis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- vulvovaginal candidiasis (VVC)
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
Source: Table 2
Description: Differential microbial abundance between controls and vulvovaginal candidiasis subjects
Abundance in Group 1: decreased abundance in Vulvovaginal candidiasis
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Lactobacillaceae | ||
| Lactobacillus |
Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
Source: Table 2
Description: Differential microbial abundance between controls and vulvovaginal candidiasis subjects
Abundance in Group 1: increased abundance in Vulvovaginal candidiasis
Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Bacterial vaginosis BACT VAGINITIDES,BACT VAGINITIS,BACT VAGINOSES,BACT VAGINOSIS,Bacterial Vaginitides,Bacterial Vaginitis,Bacterial Vaginoses,bacterial vaginosis,BV,Nonspecific Vaginitis,VAGINITIDES BACT,Vaginitides, Bacterial,VAGINITIS BACT,Vaginitis, Bacterial,Vaginitis, Nonspecific,VAGINOSES BACT,Vaginoses, Bacterial,VAGINOSIS BACT,Vaginosis, Bacterial,Bacterial vaginosis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- bacterial vaginosis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- bacterial vaginosis (BV)
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
Source: Table 2
Description: Differential microbial abundance between controls and bacterial vaginosis subjects
Abundance in Group 1: decreased abundance in bacterial vaginosis
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Lactobacillaceae | ||
| Lactobacillus |
Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
Source: Table 2
Description: Differential microbial abundance between controls and bacterial vaginosis subjects
Abundance in Group 1: increased abundance in bacterial vaginosis
Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1
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