16S rRNA gene sequencing of rectal swab in patients affected by COVID-19/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/05/25
Curated date: 2021/07/04
Curator: Claregrieve1
Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Victoria
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
- Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
- 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
- COVID-positive patients admitted to infectious disease ward (w-COVID-19)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-positive patients admitted to ICU (i-COVID-19)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
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).
- raw counts
- Statistical test
- DESeq2
- 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 Fatima on 2022/06/1
Source: Table S6, S9, S12
Description: Differential microbial abundance between ICU COVID-19 patients (i-COVID-19) and non-ICU COVID-19 patients (w-COVID-19)
Abundance in Group 1: increased abundance in COVID-positive patients admitted to ICU (i-COVID-19)
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/06/1
Source: Table S6, S9, S12
Description: Differential microbial abundance between ICU COVID-19 patients (i-COVID-19) and non-ICU COVID-19 patients (w-COVID-19)
Abundance in Group 1: decreased abundance in COVID-positive patients admitted to ICU (i-COVID-19)
Revision editor(s): Claregrieve1
