Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort/Experiment 1
Subjects
- Location of subjects
- Switzerland
- 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
- Non-Covid 19 Patients - pneumonia patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients admitted for COVID-19
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 57
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 Months
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
- 2.5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Fig. 1C
Description: C, D Differential abundance analysis and distance-based redundancy analysis (db-RDA) in COVID-19 and non-COVID-19 patients. COVID-19 and non-COVID-19 pneumonia patients were compared to evaluate the COVID-19 effect. C Differentially abundant taxa identified by linear discriminant analysis effect size (LEfSe) at genus level. The results with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented as a bar plot (**p < 0.01, ***p < 0.001).
Abundance in Group 1: increased abundance in COVID-19 Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Pseudoflavonifractor | ||
| Ruthenibacterium |
Revision editor(s): Tolulopeo, Peace Sandy
Signature 2
Source: Fig. 1c
Description: C, D Differential abundance analysis and distance-based redundancy analysis (db-RDA) in COVID-19 and non-COVID-19 patients. COVID-19 and non-COVID-19 pneumonia patients were compared to evaluate the COVID-19 effect. C Differentially abundant taxa identified by linear discriminant analysis effect size (LEfSe) at genus level. The results with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented as a bar plot (**p < 0.01, ***p < 0.001).
Abundance in Group 1: decreased abundance in COVID-19 Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Fenollaria | ||
| Finegoldia | ||
| Porphyromonas | ||
| Corynebacterium | ||
| Sutterella | ||
| Anaerococcus | ||
| Negativicoccus |
Revision editor(s): Tolulopeo, Peace Sandy
