Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection

From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Qingqing B, Jie Z, Songben Q, Juan C, Lei Z, Mu X
Journal
Microbial pathogenesis
Year
2021
Keywords:
16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression
HPV persistent infection is a main event leading to the development of cervical intraepithelial neoplasia and cervical cancer. Earlier to distinguish HPV persistent and transient infection is meaningful but the methods are limited. This study used 16S rDNA sequencing to determine the cervicovaginal microbiota of HPV persistent infection, transient infection and health women. Sequences analysis was performed and according to subsequent statistical analysis, the structure of cervicovaginal microbiota of healthy and transient infection individuals is relatively single, Firmicutes occupy the main composition. However, that of the HPV persistent infection presented a complicated trend and the abundance of Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria was higher. The significance p-values of the average species abundance of Firmicutes, Proteobacteria and Bacteroides between HPV persistent and transient infection groups were 0.003, 0.018 and 0.005, respectively. The study also found 36 biomarkers of cervicovaginal microbiota dysbiosis for LDA score>4 among different groups. At genus level, Prevotella, Sphingomonas and Anaerococcus correlated with HPV persistent infection. At species level, Lactobacillus iners correlated with HPV transient infection. Besides, local immune microenvironment was changed with cervicovaginal microbiota dysbiosis. Interleukin-6 and TNF-α were significantly upregulated in cervical secretions from HPV persistent infection compared with those from transient infection and healthy women. Peripheral blood Regulatory T cells and myeloid-derived suppressor cells in patients with HPV persistent infection were also significantly increased. In conclusion, this study identified cervicovaginal microbiota dysbiosis closely related to HPV persistent infection, which provided a new idea and method for the prevention of cervical cancer.

Experiment 1


Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2021/03/20

Curator: Cynthia Anderson

Revision editor(s): WikiWorks, Cynthia Anderson, Peace Sandy, Folakunmi

Subjects

Location of subjects
China
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
Uterine cervix Canalis cervicis uteri,Caudal segment of uterus,Cervical canal,Cervical canal of uterus,Cervix,Cervix of uterus,Cervix uteri,Neck of uterus,Uterine cervix,uterine cervix
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease,Human papilloma virus infection
Group 0 name Corresponds to the control (unexposed) group for case-control studies
HPV- controls and HPV+ transient patients
Group 1 name Corresponds to the case (exposed) group for case-control studies
HPV+ persistence
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
HPV infection of the same type that lasts for more than 12 months
Group 0 sample size Number of subjects in the control (unexposed) group
9
Group 1 sample size Number of subjects in the case (exposed) group
6
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Ion Torrent

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
LEfSe
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)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
4

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Chao1 Abundance-based estimator of species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Richness Number of species
increased

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2021/03/20

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 5

Description: LEfSe Analysis. A: LDA value distribution histogram

Abundance in Group 1: increased abundance in HPV+ persistence

NCBI Quality ControlLinks
Pseudomonadota
Alphaproteobacteria
Actinomycetota
Clostridia
Eubacteriales
Hyphomicrobiales
Bacteroidota
Bacteroidia
Gammaproteobacteria
Rhizobiaceae
Phyllobacterium
Veillonellaceae
Bacteroidales
Prevotellaceae
Sphingomonadales
Sphingomonadaceae
Sphingomonas
Anaerococcus
Sphingomonas leidyi
Prevotella
Porphyromonadaceae
Porphyromonas
Phocaeicola coprocola DSM 17136
Burkholderiaceae
Ruminiclostridium papyrosolvens
Dialister
Peptoniphilus

Revision editor(s): Cynthia Anderson

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2021/03/20

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, Folakunmi

Source: Figure 5

Description: LEfSe Analysis. A: LDA value distribution histogram

Abundance in Group 1: decreased abundance in HPV+ persistence

NCBI Quality ControlLinks
Bacilli
Bacillota
Lactobacillaceae
Lactobacillales
Lactobacillus
Lactobacillus iners

Revision editor(s): Cynthia Anderson, Folakunmi

Experiment 2


Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2021/03/20

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, WikiWorks, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
HPV- controls and HPV+ persistent patients
Group 1 name Corresponds to the case (exposed) group for case-control studies
HPV+ transient
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
HPV infection cleared within 12 months
Group 0 sample size Number of subjects in the control (unexposed) group
11
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2021/03/20

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 5

Description: LEfSe Analysis. A: LDA value distribution histogram

Abundance in Group 1: increased abundance in HPV+ transient

NCBI Quality ControlLinks
Lactobacillus iners

Revision editor(s): Cynthia Anderson

Experiment 3


Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2024/02/06

Curator: Folakunmi

Revision editor(s): Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
HPV+ transient
Group 1 name Corresponds to the case (exposed) group for case-control studies
HPV+ persistent
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients whose HPV infection persisted for 12 months
Group 0 sample size Number of subjects in the control (unexposed) group
6

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
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Richness Number of species
increased

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2024/02/06

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: supplementary figure s1

Description: Lefse analysis between persistent HPV infection group and transient HPV infection group

Abundance in Group 1: increased abundance in HPV+ persistent

NCBI Quality ControlLinks
unclassified Prevotellaceae
Burkholderiaceae
unclassified Gammaproteobacteria
Sphingomonas leidyi
Sphingomonas
Prevotellaceae
Sphingomonadaceae
Sphingomonadales
Phyllobacterium
Bacteroidales
Rhizobiaceae
Clostridia
Eubacteriales
Bacteroidia
Actinomycetota
Gammaproteobacteria
Alphaproteobacteria
Pseudomonadota

Revision editor(s): Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2024/02/06

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: supplementary figure s1

Description: Lefse analysis between persistent HPV infection group and transient HPV infection group

Abundance in Group 1: decreased abundance in HPV+ persistent

NCBI Quality ControlLinks
Bacilli
Bacillota
Lactobacillaceae
Lactobacillales
Lactobacillus
Lactobacillus iners
Bacteria

Revision editor(s): Folakunmi

Experiment 4


Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2024/02/09

Curator: Folakunmi

Revision editor(s): Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
HPV- controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
HPV+ persistence
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
HPV infection of the same type that lasts for more than 12 months
Group 0 sample size Number of subjects in the control (unexposed) group
5
Group 1 sample size Number of subjects in the case (exposed) group
6

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
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Richness Number of species
increased

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2024/02/09

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: supplementary figure s1

Description: Lefse analysis between persistent HPV infection group and transient HPV infection group

Abundance in Group 1: increased abundance in HPV+ persistence

NCBI Quality ControlLinks
Sneathia sanguinegens
Colwellia
Colwelliaceae
Cryomorphaceae
Odoribacter
Dialister
unclassified Prevotellaceae
Burkholderiaceae
unclassified Gammaproteobacteria
Prevotella
Fusobacteriales
Fusobacteriia
Enterobacteriaceae
Enterobacterales
Anaerococcus
Cyanobacteriota
Sphingomonas leidyi
Sphingomonadaceae
Sphingobacteriales
Sphingomonas
Eubacteriales
Prevotellaceae
Phyllobacterium
Rhizobiaceae
Hyphomicrobiales
Bacteroidales
Gammaproteobacteria
Bacteroidia
Veillonellaceae
Selenomonadales
Negativicutes
Actinomycetota
unclassified Actinomycetota
Alphaproteobacteria
Pseudomonadota

Revision editor(s): Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2024/02/09

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: supplementary figure s1

Description: Lefse analysis between persistent HPV infection group and transient HPV infection group

Abundance in Group 1: decreased abundance in HPV+ persistence

NCBI Quality ControlLinks
Lactobacillaceae
Lactobacillales
Lactobacillus
Bacillus
Bacillota
Lactobacillus iners

Revision editor(s): Folakunmi