Nasopharyngeal Microbiota Profiling of SARS-CoV-2 Infected Patients/Experiment 1

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Curated date: 2021/06/04

Curator: Claregrieve1

Revision editor(s): WikiWorks753, Claregrieve1


Location of subjects Country from which study subjects were recruited
Host species Species from which microbiome was sampled (if applicable)
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
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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
COVID-19 negative patients
Group 1 name Corresponds to the case (exposed) group for case-control studies
COVID-19 cases
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Diagnosis with COVID-19 based on SARS-CoV-2 RNA detection using real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay
Group 0 sample size Number of subjects in the control (unexposed) group
Group 1 sample size Number of subjects in the case (exposed) group

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
Richness Number of species