Metagenomic assessment of gut microbial communities and risk of severe COVID-19/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-23
Curated date: 2023/12/19
Curator: OdigiriGreat
Revision editor(s): OdigiriGreat, Peace Sandy, ChiomaBlessing
Subjects
- Location of subjects
- United States of America
- 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
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Moderate COVID-19
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Severe COVID-19
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Hospitalized patients with severe Covid-19
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 79
- 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
- PCR
- 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
- Random Forest Analysis
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, ethnic group, antibiotic exposure, comorbidity, race, sequence read depth, Confounders controlled for: "use of corticosteroids or remdesivir" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.use of corticosteroids or remdesivir, Confounders controlled for: "days since admission" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.days since admission, Confounders controlled for: "SARS-CoV-2 stool viral load" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.SARS-CoV-2 stool viral load, Confounders controlled for: "participant-level random effect" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.participant-level random effect
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-23
Source: Fig. 3a
Description: Stool-based classifier for COVID-19 disease severity showing the differential abundance among patients with severe/critical COVID-19 compared to patients with mild/moderate COVID-19
Abundance in Group 1: increased abundance in Severe COVID-19
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus faecalis |
Revision editor(s): Peace Sandy, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-23
Source: Fig. 3a
Description: Stool-based classifier for COVID-19 disease severity showing the differential abundance among patients with severe/critical COVID-19 compared to patients with mild/moderate COVID-19
Abundance in Group 1: decreased abundance in Severe COVID-19
Revision editor(s): Peace Sandy, ChiomaBlessing
