Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-6
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
- Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx
- 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
- samples from Healthy patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pharyngeal samples from COVID-19 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 39
- Group 1 sample size Number of subjects in the case (exposed) group
- 174
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
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-6
Source: Within Results text ("Alteration of microbial composition in COVID-19 patients is associated with disease severity", lines 1-4)
Description: Altered microbial composition associated with disease severity
Abundance in Group 1: decreased abundance in Pharyngeal samples from COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Burkholderia | ||
| Campylobacter | ||
| Escherichia | ||
| Fusobacterium | ||
| Haemophilus | ||
| Micrococcus | ||
| Neisseria | ||
| Selenomonas | ||
| Tannerella | ||
| Treponema |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-6
Source: Within Results text ("Alteration of microbial composition in COVID-19 patients is associated with disease severity", lines 1-4)
Description: Altered microbial composition associated with disease severity
Abundance in Group 1: increased abundance in Pharyngeal samples from COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Rothia | ||
| Streptococcus |
