Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- Singapore
- 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
- Sputum Expectoration,Sputum,sputum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Respiratory system disease [X]Chronic and other pulmonary manifestations due to radiation,[X]Chronic and other pulmonary manifestations due to radiation (disorder),[X]Other diseases of the respiratory system,[X]Other diseases of the respiratory system (disorder),[X]Respiratory conditions due to other specified external agents,[X]Respiratory conditions due to other specified external agents (disorder),[X]Respiratory conditions due to unspecified external agent,[X]Respiratory conditions due to unspecified external agent (disorder),ALVEOL PNEUMONOPATHY NEC,ALVEOL PNEUMONOPATHY NOS,CHR PUL MANIF D/T RADIAT,Chronic and other pulmonary manifestations due to radiation,Disease of respiratory system,disease of respiratory system,Disease of respiratory system (disorder),Disease of respiratory system, NOS,disease or disorder of respiratory system,DISEASES OF THE RESPIRATORY SYSTEM,Disorder of respiratory system,disorder of respiratory system,Disorder of respiratory system (disorder),INORG DUST PNEUMOCON NEC,LUNG INVOLV IN OTH DIS,Lung involvement in conditions classified elsewhere,Lung involvement in other diseases classified elsewhere,MEDIASTINUM DISEASE NEC,Other alveolar and parietoalveolar pneumonopathy,Other diseases of mediastinum, not elsewhere classified,Other diseases of respiratory system,Other diseases of respiratory system NOS,Other diseases of respiratory system NOS (disorder),Other diseases of respiratory system, not elsewhere classified,Other diseases of trachea and bronchus, not elsewhere classified,Other respiratory system diseases,Other respiratory system diseases (disorder),Other respiratory system diseases NOS,Other respiratory system diseases NOS (disorder),Other specified alveolar and parietoalveolar pneumonopathies,PNEUMOCONIOSES AND OTHER LUNG DISEASES DUE TO EXTERNAL AGENTS,Pneumoconiosis due to other inorganic dust,RESP COND: EXT AGENT NEC,RESP COND: EXT AGENT NOS,RESP SYSTEM DISEASE NEC,RESP SYSTEM DISEASE NOS,Respiratory conditions due to other and unspecified external agents,Respiratory conditions due to other specified external agents,Respiratory conditions due to unspecified external agent,Respiratory disease,respiratory disease,Respiratory disorder,respiratory disorder,Respiratory disorder, NOS,respiratory system disease,respiratory system disease or disorder,Respiratory system diseases NOS,Respiratory system diseases NOS (disorder),Respiratory System Disorder,respiratory system disorder,Unspecified alveolar and parietoalveolar pneumonopathy,Unspecified disease of respiratory system,Respiratory system disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-diseased/ healthy individuals (ND)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diseased individuals (D)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with a range of chronic respiratory disease states (severe asthma, chronic obstructive pulmonary disease- COPD, and bronchiectasis)
- 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
- 41
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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).
- 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
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Needs review
Source: Supplemental. fig. E3D and Supplemental fig. E3E
Description: Differential microbial abundance between diseased (D) and nondiseased (ND)/ healthy individuals
Abundance in Group 1: increased abundance in Diseased individuals (D)
| NCBI | Quality Control | Links |
|---|---|---|
| Arachnia | ||
| Bifidobacterium | ||
| Corynebacterium | ||
| Escherichia | ||
| Haemophilus | ||
| Klebsiella | ||
| Paenibacillus | ||
| Pseudomonas | ||
| Psychrobacter | ||
| Tannerella | ||
| Rothia mucilaginosa |
Revision editor(s): ChiomaBlessing
Signature 2
Needs review
Source: Supplemental. fig. E3D and Supplemental fig. E3E
Description: Differential microbial abundance between diseased (D) and nondiseased (ND)/ healthy individuals
Abundance in Group 1: decreased abundance in Diseased individuals (D)
Revision editor(s): ChiomaBlessing
