HPV infection and bacterial microbiota in breast milk and infant oral mucosa
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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
Tuominen H, Rautava S, Collado MC, Syrjänen S, Rautava J
Journal
PloS one
Year
2018
OBJECTIVE: We investigated the association between bacterial microbiota in breast milk and the infant mouth. The influence of human papilloma virus (HPV) infection on infant oral microbiota was also assessed. MATERIAL AND METHODS: Altogether 35 breast milk and 35 infant oral samples with known HPV status were selected from the Finnish Family HPV Study cohort. In total, there were 31 mother-infant pairs. The microbiota composition was characterized by 16S rRNA gene sequencing (V3-V4 region). RESULTS: HPV DNA was present in 8.6% (3/35) of the breast milk and 40% (14/35) of the infant oral samples. Eight shared genera between breast milk and infant oral were found; these included Streptococcus, Staphylococcus, Unclassified Gemellaceae, Rothia, Veillonella, Haemophilus, Propionibacterium and Corynebacterium. HPV status was not associated with either microbiota richness or diversity in the infant mouth. However, the infant oral microbiota clustered in different groups according to HPV status. We detected higher abundance of Veillonella dispar (p = 0.048) at species level in HPV negative infant oral samples. We did not detect differences in the breast milk microbiota composition related to HPV infection due to only three HPV positive milk samples. CONCLUSIONS: HPV infection is associated with distinct oral bacterial microbiota composition in infants. The direction of causality underlying the phenomenon remains unclear.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/4
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
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/4
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
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/4
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
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/4
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/4
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
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/4
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
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/4
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/4
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
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