Microbiome analysis in individuals with human papillomavirus oral infection
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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.
URI
Authors
Journal
Sci. Rep.
Year
Pages:
13
First page:
Introduction"Introduction" is not a number.
Keywords:
Microbiome , HIV, Human Papillomavirus
This study looked at how the oral microbiome (the bacteria in the mouth) is affected by human papillomavirus (HPV) infection, especially in people with and without HIV. Researchers analyzed mouth rinse samples from 63 men, comparing their bacterial composition based on whether they had HPV and/or HIV.
They found that HPV infection changes the diversity and types of bacteria in the mouth, but these changes were different depending on whether the person also had HIV. In HIV-negative individuals, certain bacteria were more common when HPV was present, while in HIV-positive individuals, different bacterial shifts were observed.
The study suggests that HPV infection interacts with the oral microbiome in unique ways, and this interaction may be influenced by HIV status.
Experiment 1
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
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- 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
- HIV-/HPV- (Human immuno deficiency virus negative/Human papilloma virus negative)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-/hrHPV+ (Human immuno deficiency virus negative/ High risk human papilloma virus positive)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV (Human Immunodeficiency Virus) negative Patients with High risk human papillomavirus (HPV) oral infection.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
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).
- raw counts
- Statistical test
- Linear Regression
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, alcohol consumption measurement, smoking status, oral hygiene, Matched on: "HIV status" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.HIV status
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, Confounders controlled for: "sexual behaviour" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sexual behaviour, education level, household income, alcohol consumption measurement, oral hygiene, Confounders controlled for: "STI history" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.STI history, smoking status
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 4, supplementary Figure 2
Description: Differential abundance of oral bacterial taxa at the genus and species level.
Abundance in Group 1: increased abundance in HIV-/hrHPV+ (Human immuno deficiency virus negative/ High risk human papilloma virus positive)
Signature 2
Source: Figure 4, supplementary Figure 2
Description: Differential abundance of oral bacteria taxa at the genus and specie level.
Abundance in Group 1: decreased abundance in HIV-/hrHPV+ (Human immuno deficiency virus negative/ High risk human papilloma virus positive)
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV+/HPV- (Human immuno deficiency virus positive / Human papilloma virus negative)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV+/hrHPV+ (Human immuno deficiency virus positive/ High risk Human papilloma virus positive)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV (Human Immunodeficiency Virus) positive Patients with High risk human papillomavirus (HPV) oral infection.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, alcohol consumption measurement, smoking status, oral hygiene, Matched on: "HIV status" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.HIV status, Matched on: "cART therapy" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.cART therapy
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, education level, household income, Confounders controlled for: "sexual behaviour" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sexual behaviour, Confounders controlled for: "STI history" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.STI history, smoking status, oral hygiene, alcohol consumption measurement
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 4, supplementary Figure 2
Description: Differential abundance of oral bacteria taxa at the genus and specie level.
Abundance in Group 1: increased abundance in HIV+/hrHPV+ (Human immuno deficiency virus positive/ High risk Human papilloma virus positive)
Signature 2
Source: Figure 4, supplementary Figure 2
Description: Differential abundance of oral bacteria taxa at the genus and specie level.
Abundance in Group 1: decreased abundance in HIV+/hrHPV+ (Human immuno deficiency virus positive/ High risk Human papilloma virus positive)
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