Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women

From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Ritu W, Enqi W, Zheng S, Wang J, Ling Y, Wang Y
Journal
Cancer prevention research (Philadelphia, Pa.)
Year
2019
The aim of this study was to investigate the associations between cervical microbiota and different human papillomavirus (HPV) infection statuses in cytologically normal women. The cervical microbiota of HPV-positive or -negative women with a normal cytologic diagnosis was characterized and compared using 16S rDNA-based high-throughput sequencing, and the differences in cervical microbiota associated with new acquisition, persistence, and clearances of HPV genotypes were analyzed via one-year follow-up. The results showed that the cervical microbial richness of HPV-positive women was lower than for HPV-negative women, and the difference was more significant in the postmenopausal group relative to the premenopausal group. Ureaplasma parvum and related taxa were associated with baseline HPV positivity, while Brochothrix, Diplorickettsia, Ezakiella, Faecalibacterium, and Fusobacterium genera and their related taxa and Pseudomonas aeruginosa were associated with baseline HPV negativity. For HPV-positive women, the baseline abundance of Actinomyces was negatively associated with new HPV infection, Alloprevotella tannerae, Prevotella nigrescens, and Prevotella oulorum; and Dialister invisus were positively associated with new HPV-type infection within the year of follow-up. Lactobacillus delbrueckii was found to be negatively associated with persistent HPV infection and 9 taxa belonging to Prevotella, Dialister, and Lachnospiraceae were found to be positively associated with persistence, and/or negatively associated with clearance of HPV types. We also observed 10 novel taxa associated with the clearance/persistence of HPV that had not been reported elsewhere. Those taxa associated with different infection statuses of HPV could be used as a biomarker to help predict the risk of developing persistent HPV infection.

Experiment 1


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled (if applicable)
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
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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Baseline HPV-
Group 1 name Corresponds to the case (exposed) group for case-control studies
Baseline HPV+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
HPV+ confirmed by HPV assay and genotyping
Group 0 sample size Number of subjects in the control (unexposed) group
43
Group 1 sample size Number of subjects in the case (exposed) group
90
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 weeks

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
Illumina

Statistical Analysis

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)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks

Source: Figure 3

Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status

Abundance in Group 1: increased abundance in Baseline HPV+

NCBI Quality ControlLinks
Mollicutes
Mycoplasmatota
Mycoplasmatales
Mycoplasmataceae
Ureaplasma

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks, Merit

Source: figure 3

Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status

Abundance in Group 1: decreased abundance in Baseline HPV+

NCBI Quality ControlLinks
Coxiellaceae
Deinococci
Deinococcota
Ectothiorhodospiraceae
Ezakiella
Faecalibacterium
Fusobacteriaceae
Fusobacterium
Listeriaceae
Rickettsiella
Fusobacteriales

Revision editor(s): WikiWorks, Merit

Experiment 2


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
no new acquisition of HPV within a year
Group 1 name Corresponds to the case (exposed) group for case-control studies
new acquisition of HPV within a year
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
New HPV-type acquisition confirmed by HPV assay and genotyping
Group 0 sample size Number of subjects in the control (unexposed) group
109
Group 1 sample size Number of subjects in the case (exposed) group
24

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

Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks

Source: figure 3

Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status

Abundance in Group 1: decreased abundance in new acquisition of HPV within a year

NCBI Quality ControlLinks
Actinomyces

Revision editor(s): WikiWorks

Experiment 3


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
with at least one HPV type cleared in a year
Group 1 name Corresponds to the case (exposed) group for case-control studies
without any HPV type cleared
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
No HPV-type cleared confirmed by HPV assay and genotyping
Group 0 sample size Number of subjects in the control (unexposed) group
75
Group 1 sample size Number of subjects in the case (exposed) group
15

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

Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks

Source: figure 3

Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status

Abundance in Group 1: decreased abundance in without any HPV type cleared

NCBI Quality ControlLinks
Paracoccaceae
Rhodobacterales

Revision editor(s): WikiWorks

Experiment 4


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
HPV-
Group 1 name Corresponds to the case (exposed) group for case-control studies
HPV+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
HPV+ confirmed by HPV assay and genotyping
Group 0 sample size Number of subjects in the control (unexposed) group
43
Group 1 sample size Number of subjects in the case (exposed) group
90

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

Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks

Source: figure 3

Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level

Abundance in Group 1: increased abundance in HPV+

NCBI Quality ControlLinks
Ureaplasma parvum

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks

Source: figure 3

Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level

Abundance in Group 1: decreased abundance in HPV+

NCBI Quality ControlLinks
Ezakiella massiliensis
Pseudomonas aeruginosa

Revision editor(s): WikiWorks

Experiment 5


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
no new acquisition of HPV within a year
Group 1 name Corresponds to the case (exposed) group for case-control studies
new acquisition of HPV within a year
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
New HPV-type acquisition confirmed by HPV assay and genotyping
Group 0 sample size Number of subjects in the control (unexposed) group
109
Group 1 sample size Number of subjects in the case (exposed) group
24

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

Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks

Source: figure 3

Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level

Abundance in Group 1: increased abundance in new acquisition of HPV within a year

NCBI Quality ControlLinks
Alloprevotella tannerae
Prevotella nigrescens
Prevotella oulorum
Dialister invisus

Revision editor(s): WikiWorks

Experiment 6


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
with any HPV type cleared in a year
Group 1 name Corresponds to the case (exposed) group for case-control studies
without any HPV type cleared
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
No HPV-type cleared confirmed by HPV assay and genotyping
Group 0 sample size Number of subjects in the control (unexposed) group
75
Group 1 sample size Number of subjects in the case (exposed) group
15

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

Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks

Source: figure 3

Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level

Abundance in Group 1: increased abundance in without any HPV type cleared

NCBI Quality ControlLinks
Gemella asaccharolytica
Prevotella amnii
Labilithrix luteola
Lachnotalea glycerini

Revision editor(s): WikiWorks

Experiment 7


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
no HPV type persisted
Group 1 name Corresponds to the case (exposed) group for case-control studies
at least one HPV type persisted
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Any HPV-type persisted confirmed by HPV assay and genotyping
Group 0 sample size Number of subjects in the control (unexposed) group
64
Group 1 sample size Number of subjects in the case (exposed) group
29

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

Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks

Source: figure 3

Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level

Abundance in Group 1: increased abundance in at least one HPV type persisted

NCBI Quality ControlLinks
Hoylesella timonensis
Microvirga lupini
Dialister invisus
Coprococcus comes
Deinococcus radiopugnans
Anaerobacterium chartisolvens

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks

Source: figure 3

Description: Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level

Abundance in Group 1: decreased abundance in at least one HPV type persisted

NCBI Quality ControlLinks
Lactobacillus delbrueckii

Revision editor(s): WikiWorks