HPV infection and bacterial microbiota in breast milk and infant oral mucosa/Experiment 2

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

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 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

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

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

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 Control	Links
Lysinibacillus
Ureaplasma

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

EditHistoryDelete

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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 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