Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients/Experiment 2
From BugSigDB
Needs review
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 , Throat Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx,Gula,Throat,throat
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Abnormality of the respiratory system Respiratory abnormality,Abnormality of the respiratory system,abnormality of the respiratory system
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- local controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-Covid-19 Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Hospitalized non-COVID-19 patients with respiratory symptoms or related illnesses.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 69
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 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
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Fig 2B
Description: Linear discriminant analysis (LDA) effect size (LEfSe) identifying discriminative bacterial genera (B) between hospitalized non-COVID patients and local controls.
Abundance in Group 1: increased abundance in Non-Covid-19 Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Atopobium | ||
| Dolosigranulum | ||
| Lacticaseibacillus | ||
| Lactobacillus | ||
| Ligilactobacillus | ||
| Limosilactobacillus | ||
| Megasphaera | ||
| Prevotella | ||
| Rothia | ||
| Veillonella | ||
| Prevotella sp. 1-8 |
Revision editor(s): Abiola-Salako
Signature 2
Needs review
Source: Fig 2B
Description: Linear discriminant analysis (LDA) effect size (LEfSe) identifying discriminative bacterial genera(B) between hospitalized non-COVID patients and local controls.
Abundance in Group 1: decreased abundance in Non-Covid-19 Patients
Revision editor(s): Abiola-Salako
