Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19/Experiment 1
Curated date: 2021/03/04
Curator: Fatima
Revision editor(s): WikiWorks, Fatima, Claregrieve1, Peace Sandy, Davvve
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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
- Patients with low-to-none SARS CoV-2 infectivity
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with high SARS CoV-2 infectivity
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SARS CoV-2 infection confirmed by two consecutive RT-OCR tests. High SARS-CoV2 infectivity defined as higher 3' vs 5', end coverage of SARS CoV-2 genome in fecal viral RNA metagenome.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Source: Figure 4
Description: Differential bacterial species and functional capacities between feces with high severe acute respiratory syndrome coronavirus 2 infectivity and feces with low to-none SARS-CoV-2 infectivity
Abundance in Group 1: decreased abundance in Patients with high SARS CoV-2 infectivity
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides stercoris | ||
| Lachnospiraceae bacterium | ||
| Parabacteroides merdae | ||
| Alistipes onderdonkii |
Revision editor(s): Fatima, Claregrieve1
Signature 2
Source: Figure 4
Description: Differential bacterial species and functional capacities between feces with high severe acute respiratory syndrome coronavirus 2 infectivity and feces with low to-none SARS-CoV-2 infectivity
Abundance in Group 1: increased abundance in Patients with high SARS CoV-2 infectivity
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella aerofaciens | ||
| Collinsella tanakaei | ||
| Morganella morganii | ||
| Streptococcus infantis |
Revision editor(s): Fatima, Claregrieve1
