The active lung microbiota landscape of COVID-19 patients through the metatranscriptome data analysis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-14
Curated date: 2021/06/11
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Peace Sandy
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
- COVID-19 2019 novel coronavirus,2019 novel coronavirus infection,2019-nCoV,2019-nCoV infection,beta-CoV,beta-CoVs,betacoronavirus,coronavirus disease 2019,SARS-coronavirus 2,SARS-CoV-2,severe acute respiratory syndrome coronavirus 2,severe acute respiratory syndrome coronavirus 2 infectious disease,β-coronavirus,β-CoV,β-CoVs,COVID-19,cOVID-19
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 infected patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- NIL
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
- Sequencing platform: "IDseq" is not in the list (DNA-DNA Hybridization, Human Intestinal Tract Chip, Illumina, Ion Torrent, Non-quantitative PCR, PacBio RS, PhyloChip, Roche454, RT-qPCR, Mass spectrometry, ...) of allowed values.IDseq
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- 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
- increased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-14
Source: Supplementary Table 2
Description: Differential microbial abundance between the COVID-19 patients and the healthy controls
Abundance in Group 1: increased abundance in COVID-19 cases
Revision editor(s): Claregrieve1, Davvve
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-14
Curated date: 2021/06/12
Curator: Claregrieve1
Revision editor(s): Claregrieve1, Davvve, Peace Sandy
Source: Supplementary Table 2
Description: Differential microbial abundance between the COVID-19 patients and the healthy controls
Abundance in Group 1: decreased abundance in COVID-19 cases
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter rectus | ||
| Campylobacter showae | ||
| Treponema putidum | ||
| Lachnoclostridium phytofermentans |
Revision editor(s): Claregrieve1, Davvve, Peace Sandy
