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

Study information

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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

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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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. 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

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

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

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

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

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Micrococcaceae
Rothia
Rothia mucilaginosa
Streptococcaceae
Streptococcus
Veillonella
Veillonella dispar
Weeksellaceae
Haemophilus
Anaerococcus sp.
Finegoldia

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Signature 2

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

Curated date: 2021/01/10

Curator: Fatima Zohra

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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

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Agrobacterium
Bacteroides
Delftia
Lactobacillus
Megasphaera
Propionibacterium
Pseudomonas
Staphylococcus
Tissierellaceae

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Experiment 2

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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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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

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

Curated date: 2021/01/10

Curator: Fatima Zohra

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Source: Figure 5F

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

Abundance in Group 1: increased abundance in HPV+

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Lysinibacillus
Ureaplasma

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Signature 2

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

Curated date: 2021/01/10

Curator: Fatima Zohra

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Source: Figure 5F

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

Abundance in Group 1: decreased abundance in HPV+

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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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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

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

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

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

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Veillonellaceae
Veillonella dispar

Revision editor(s): WikiWorks