Diversity of vaginal microbiome and metabolome during genital infections

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
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

Curated date: 2023/03/08

Curator: Danyab56

Revision editor(s): LGeistlinger, Claregrieve1, Danyab56

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

Curated date: 2023/03/09

Curator: Danyab56

Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1

Source: Table 2

Description: Differential microbial abundance between controls and chlamydia subjects

Abundance in Group 1: increased abundance in Chlamydia trachomatis

NCBI Quality ControlLinks
Aerococcaceae
Aerococcus
Alloscardovia
Atopobium
Bifidobacteriaceae
Blautia
Clostridiaceae
Clostridium
Coriobacteriaceae
Dialister
Escherichia
Faecalibacterium
Lachnospiraceae
Megasphaera
Oscillospiraceae
Roseburia
Sneathia
Streptococcus
Ureaplasma
Veillonellaceae
unclassified Coriobacteriaceae
unclassified Lachnospiraceae
Bifidobacterium

Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/09

Curator: Danyab56

Revision editor(s): Danyab56, Claregrieve1

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

Curated date: 2023/03/09

Curator: Danyab56

Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1

Source: Table 2

Description: Differential microbial abundance between controls and vulvovaginal candidiasis subjects

Abundance in Group 1: decreased abundance in Vulvovaginal candidiasis

NCBI Quality ControlLinks
Bacillota
Lactobacillaceae
Lactobacillus

Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/09

Curator: Danyab56

Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1

Source: Table 2

Description: Differential microbial abundance between controls and vulvovaginal candidiasis subjects

Abundance in Group 1: increased abundance in Vulvovaginal candidiasis

NCBI Quality ControlLinks
Actinomycetaceae
Actinomycetota
Alloscardovia
Atopobium
Bacteroidia
Bifidobacteriaceae
Blautia
Coriobacteriaceae
Dialister
Escherichia
Faecalibacterium
Finegoldia
Gardnerella
Lachnospiraceae
Megasphaera
Oscillospiraceae
Peptostreptococcaceae
Peptostreptococcus
Prevotella
Prevotellaceae
Roseburia
Streptococcus
Tissierellaceae
Veillonella
Veillonellaceae
Xanthomonas
unclassified Coriobacteriaceae

Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1

Experiment 3


Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/09

Curator: Danyab56

Revision editor(s): Danyab56, Claregrieve1

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

Curated date: 2023/03/09

Curator: Danyab56

Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1

Source: Table 2

Description: Differential microbial abundance between controls and bacterial vaginosis subjects

Abundance in Group 1: decreased abundance in bacterial vaginosis

NCBI Quality ControlLinks
Bacillota
Lactobacillaceae
Lactobacillus

Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/09

Curator: Danyab56

Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1

Source: Table 2

Description: Differential microbial abundance between controls and bacterial vaginosis subjects

Abundance in Group 1: increased abundance in bacterial vaginosis

NCBI Quality ControlLinks
Actinomycetaceae
Aerococcaceae
Aerococcus
Atopobium
Clostridiaceae
Clostridium
Coriobacteriaceae
Dialister
Gardnerella
Gemella
Lachnospiraceae
Leptotrichiaceae
Megasphaera
Mobiluncus
Peptostreptococcaceae
Peptostreptococcus
Prevotella
Prevotellaceae
Rebutia arenacea
Roseburia
Sneathia
Tissierellaceae
Typhloplanidae
Ureaplasma
Veillonellaceae
unclassified Coriobacteriaceae

Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1