Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19/Experiment 2

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Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Subjects

Location of subjects

Spain

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

NasopharynxNasopharynx

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

COVID-19COVID-19

Group 0 name Corresponds to the control (unexposed) group for case-control studies

COVID-19 negative controls

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

Severe COVID-19 patients requiring ICU

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

Patients with confirmed COVID-19 infection and severe symptoms who were admitted into the intensive care unit

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

18

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

19

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).

raw counts

Statistical test

Linear Regression

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.25

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Yes

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment

age, sex

Signature 1

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Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

Source: Supplemental Table S5

Description: Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients requiring ICU care

Abundance in Group 1: increased abundance in Severe COVID-19 patients requiring ICU

NCBI	Quality Control	Links
Treponema

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

EditHistoryDelete

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Your review change was submitted

Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

Source: Supplemental Table S5

Description: Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients requiring ICU care

Abundance in Group 1: decreased abundance in Severe COVID-19 patients requiring ICU

NCBI	Quality Control	Links
uncultured phototrophic eukaryote

Revision editor(s): Claregrieve1, WikiWorks