Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-11-5
Subjects
- Location of subjects
- China
- 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
- Lung Pulmo,Lung,lung
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lower respiratory tract disease disease of lower respiratory tract,disease or disorder of lower respiratory tract,disorder of lower respiratory tract,lower respiratory tract disease,lower respiratory tract disease or disorder,lower respiratory tract disorder,Lower respiratory tract disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-lower respiratory tract infections (LRTIs)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lower respiratory tract infections (LRTIs)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects who met clinical or microbiologic diagnosis criteria for lower respiratory tract infections (LRTIs).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- raw counts
- Statistical test
- edgeR
- 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
- Chao1 Abundance-based estimator of 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 Folakunmi on 2024-11-5
Source: Figure 2D and Dataset S4
Description: Barplot of the differential ambulance of micro-species between LRTIs and Non-LRTIs plotted by R
Abundance in Group 1: increased abundance in Lower respiratory tract infections (LRTIs)
Revision editor(s): Martha KJ, Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-11-5
Source: Figure 2D and Dataset S4
Description: Barplot of the differential abundance of micro species between LTRIs and Non-LTRIs plotted by R
Abundance in Group 1: decreased abundance in Lower respiratory tract infections (LRTIs)
| NCBI | Quality Control | Links |
|---|---|---|
| Bowdeniella nasicola | ||
| Corynebacterium dentalis | ||
| Filifactor alocis | ||
| Porphyromonas gingivalis | ||
| Treponema denticola | ||
| Leptotrichia hofstadii |
Revision editor(s): Martha KJ, Aleru Divine
