Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19/Experiment 3

From BugSigDB


Reviewed Marked as Reviewed by Atrayees on 2023-7-26

Curated date: 2021/07/14

Curator: Claregrieve1

Revision editor(s): WikiWorks, Claregrieve1, Atrayees

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
Oropharynx 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
Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Flu patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with influenza B
Group 0 sample size Number of subjects in the control (unexposed) group
29
Group 1 sample size Number of subjects in the case (exposed) group
31

Lab analysis

Sequencing type
WMS
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
MGISEQ-2000

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
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
increased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-26

Curated date: 2021/07/14

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 4c

Description: Differential microbial abundance between flu patients and healthy controls

Abundance in Group 1: increased abundance in Flu patients

NCBI Quality ControlLinks
Veillonella
Liquorilactobacillus nagelii
Limosilactobacillus fermentum
Prevotella amnii

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-26

Curated date: 2021/07/14

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 4c

Description: Differential microbial abundance between flu patients and healthy controls

Abundance in Group 1: decreased abundance in Flu patients

NCBI Quality ControlLinks
Oribacterium
Arachnia
Rothia
Mobiluncus
Rothia sp. HSID18069
Oribacterium sp. oral taxon 108
Arachnia propionica

Revision editor(s): Claregrieve1