Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + /Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2023/10/17

Curator: Fortunehechi

Revision editor(s): LGeistlinger, Peace Sandy, Folakunmi, Fortunehechi

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

Nasal cavity Cavitas nasalis,Cavitas nasi,Cavity of nose,Cavity of olfactory apparatus,Cavum nasi,Nasal canal,Nasal conduit space,Nasal fossa,Nasal pit,Olfactory cavity,Olfactory chamber,Olfactory chamber cavity,Olfactory pit,Nasal cavity,nasal cavity

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

Asymptomatic patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Symptomatic patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Symptomatic patients with signs of COVID-19

Group 0 sample size Number of subjects in the control (unexposed) group

36

Group 1 sample size Number of subjects in the case (exposed) group

156

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

Patients were excluded from the study if they had received antibiotics within 4 weeks of enrollment.

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

MaAsLin2

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

Pielou Quantifies how equal the community is numerically

unchanged

Richness Number of species

unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged