The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Subjects
- Location of subjects
- Portugal
- 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
- Nasopharyngeal gland , Saliva Nasopharyngeal gland,nasopharyngeal gland,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Streptococcus pneumoniae Diplococcus pneumoniae,Micrococcus pneumoniae,Streptococcus pneumoniae,streptococcus pneumoniae
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pneumococcal non-carriers.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pneumococcal carriers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals who carry pneumococci in the nasopharynx
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- MGISEQ-2000
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S2.
Description: Bacteria (ASV) differentially present in the nasopharyngeal microbiota of pneumococcal carriers and non-carriers.
Abundance in Group 1: increased abundance in Pneumococcal carriers
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus pneumoniae | ||
| Streptococcus pseudopneumoniae | ||
| Streptococcus mitis | ||
| Haemophilus influenzae | ||
| Fusobacterium nucleatum | ||
| Parvimonas micra |
Revision editor(s): Karen254., Chloe, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S2
Description: Bacteria (ASV) differentially present in the nasopharyngeal microbiota of pneumococcal carriers and non-carriers.
Abundance in Group 1: decreased abundance in Pneumococcal carriers
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parahaemolyticus | ||
| Neisseria sicca | ||
| Anaerococcus | ||
| Staphylococcus lugdunensis | ||
| Hoylesella buccalis |
Revision editor(s): Karen254., Chloe, Peace Sandy
