Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-21
Curated date: 2021/07/01
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Atrayees
Subjects
- Location of subjects
- Italy
- 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 , Oropharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx,Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx,oropharynx
- 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
- Patients infected with other human coronaviruses
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ICU COVID-19 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 patients admitted to intensive care unit
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V2-V9
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Kruskall-Wallis
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-21
Source: Table S1
Description: Differential abundance of microbial taxa between non-COVID coronavirus patients and ICU COVID patients
Abundance in Group 1: decreased abundance in ICU COVID-19 patients
Revision editor(s): Claregrieve1, Atrayees
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-21
Source: Table S1
Description: Differential abundance of microbial taxa between non-COVID coronavirus patients and ICU COVID patients
Abundance in Group 1: increased abundance in ICU COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Lactococcus | ||
| Salmonella | ||
| Scardovia | ||
| Serratia | ||
| unclassified Campylobacterales | ||
| Clostridiales Family XIII bacterium | ||
| unclassified Enterococcaceae | ||
| unclassified Pseudomonadaceae |
Revision editor(s): Claregrieve1
