HPV infection and bacterial microbiota in breast milk and infant oral mucosa

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/4

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

30395655

DOI Digital object identifier for electronic documents.

10.1371/journal.pone.0207016

URI Uniform resource identifier for web resources.

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

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Curated date: 2021/01/10

Curator: WikiWorks

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Subjects

Location of subjects: Finland

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: 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

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,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

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

Experiment 2

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Curated date: 2021/01/10

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Subjects

Location of subjects: Finland

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: 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

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: 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

Sequencing type: 16S

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: 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

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Source: Figure 5F

Description: Differential microbial abundance between HPV+ and HPV- infants

Abundance in Group 1: increased abundance in HPV+

NCBI	Links
Lysinibacillus
Ureaplasma

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Signature 2

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Source: Figure 5F

Description: Differential microbial abundance between HPV+ and HPV- infants

Abundance in Group 1: decreased abundance in HPV+

NCBI	Links
Veillonella

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Experiment 3

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Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/4

Curated date: 2021/01/10

Curator: WikiWorks

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Subjects

Location of subjects: Finland

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: 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

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: 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

Sequencing type: 16S

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

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