Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2021/06/30
Curated date: 2021/06/03
Curator: Claregrieve1
Revision editor(s): WikiWorks, Fatima, Claregrieve1, 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
- 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
- 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
- viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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
- 3.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2021/06/30
Source: Figure 3a
Description: Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls
Abundance in Group 1: increased abundance in COVID-19 cases
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Rothia | ||
| Veillonella | ||
| Thomasclavelia | ||
| Actinomyces |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Fatima on 2021/06/30
Source: Figure 3a
Description: Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls
Abundance in Group 1: decreased abundance in COVID-19 cases
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Anaerobutyricum hallii | ||
| Anaerostipes | ||
| Dorea | ||
| Faecalibacterium | ||
| Fusicatenibacter | ||
| Intestinibacter | ||
| Klebsiella | ||
| Romboutsia | ||
| Turicibacter | ||
| [Ruminococcus] torques | ||
| Clostridium |
Revision editor(s): Fatima, Claregrieve1
