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

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

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

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

NCBI Quality ControlLinks
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

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: decreased abundance in two months

NCBI Quality ControlLinks
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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

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

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 5F

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

Abundance in Group 1: increased abundance in HPV+

NCBI Quality ControlLinks
Lysinibacillus
Ureaplasma

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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 5F

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

Abundance in Group 1: decreased abundance in HPV+

NCBI Quality ControlLinks
Veillonella

Revision editor(s): Claregrieve1, WikiWorks

Experiment 3


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

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

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

NCBI Quality ControlLinks
Veillonellaceae
Veillonella dispar

Revision editor(s): WikiWorks