HPV infection and bacterial microbiota in breast milk and infant oral mucosa
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Finland
- 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 , Age 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,Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- at birth
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- two months
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infants with HPV infection at 2 months of age
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
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
- 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
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 2D, text
Description: Differential microbial abundance between samples at birth and after 2 months
Abundance in Group 1: increased abundance in two months
NCBI | Quality Control | Links |
---|---|---|
Micrococcaceae | ||
Rothia | ||
Rothia mucilaginosa | ||
Streptococcaceae | ||
Streptococcus | ||
Veillonella | ||
Veillonella dispar | ||
Weeksellaceae | ||
Haemophilus | ||
Anaerococcus sp. | ||
Finegoldia |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Figure 2D, text
Description: Differential microbial abundance between samples at birth and after 2 months
Abundance in Group 1: decreased abundance in two months
NCBI | Quality Control | Links |
---|---|---|
Agrobacterium | ||
Bacteroides | ||
Delftia | ||
Lactobacillus | ||
Megasphaera | ||
Propionibacterium | ||
Pseudomonas | ||
Staphylococcus | ||
Tissierellaceae |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Subjects
- 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-
- 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
- infants that were positive for HPV infection
- 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
- 14
Lab analysis
Statistical Analysis
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 5F
Description: Differential microbial abundance between HPV+ and HPV- infants
Abundance in Group 1: increased abundance in HPV+
NCBI | Quality Control | Links |
---|---|---|
Lysinibacillus | ||
Ureaplasma |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Figure 5F
Description: Differential microbial abundance between HPV+ and HPV- infants
Abundance in Group 1: decreased abundance in HPV+
NCBI | Quality Control | Links |
---|---|---|
Veillonella |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV- at two months
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPV+ at two months
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV+ infants at two months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
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
- decreased
Signature 1
Source: text
Description: effect of age on infant oral HPV infection and bacterial microbiota
Abundance in Group 1: decreased abundance in HPV+ at two months
NCBI | Quality Control | Links |
---|---|---|
Veillonellaceae | ||
Veillonella dispar |
Revision editor(s): WikiWorks