Integrated gut virome and bacteriome dynamics in COVID-19 patients/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
Curated date: 2021/07/02
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Victoria
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
- Antibiotic-naive COVID-19 patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antibiotic-treated COVID-19 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with COVID-19 treated with antibiotics
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
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
- Linear Regression
- 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 Atrayees on 2023-7-10
Source: Figure 3g
Description: Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and antibiotic-treated COVID-19 patients
Abundance in Group 1: increased abundance in Antibiotic-treated COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella parvula | ||
| unclassified Coprobacillus | ||
| Thomasclavelia ramosa |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
Source: Figure 3g
Description: Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and antibiotic-treated COVID-19 patients
Abundance in Group 1: decreased abundance in Antibiotic-treated COVID-19 patients
Revision editor(s): Claregrieve1
