HPV infection and bacterial microbiota in breast milk and infant oral mucosa/Experiment 1
From BugSigDB
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
