Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-3-25
Curated date: 2024/03/08
Curator: Leenaa
Revision editor(s): Svetlana up, Folakunmi, Omojokunoluwatomisin, Leenaa
Subjects
- Location of subjects
- India
- 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
- Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- COVID-19 symptoms measurement COVID-19 symptoms measurement,cOVID-19 symptoms measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mild
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- moderate
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients showing breathing difficulty with SpO2 levels ranging between 91% and 93%.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
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
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-3-25
Source: Figure 3i-j
Description: Differentially abundant bacterial species between mild group and moderate group
Abundance in Group 1: decreased abundance in moderate
| NCBI | Quality Control | Links |
|---|---|---|
| Halomonas sp. | ||
| Schaalia meyeri |
Revision editor(s): Leenaa
