Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + /Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-17
Curated date: 2023/10/23
Curator: Fortunehechi
Revision editor(s): Fortunehechi, LGeistlinger, Folakunmi
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 , Pneumonia 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,acute pneumonia,chest infection due to pneumonia,pneumonia,Pneumonia (disorder),Pneumonia (disorder) [Ambiguous],Pneumonia due to other specified organism,Pneumonia due to other specified organisms,Pneumonia due to other specified organisms (disorder),Pneumonia NOS,Pneumonia NOS (disorder),pneumonia with infectious disease,Pneumonitis,Pneumonitis (disorder),Pneumonia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- COVID-19 patients with mild pneumonia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 patients with severe pneumonia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 patients with severe pneumonia. Severe pneumonia is a type of pneumonia that is characterized by inflammation of the lungs, difficulty breathing, and low oxygen levels in the blood. It can be a life-threatening condition. This was the most exposed group in the study
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 89
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-17
Source: Table 3
Description: MaAsLin2 differentially abundant taxa analysis in COVID patients with pneumonia
Abundance in Group 1: increased abundance in COVID-19 patients with severe pneumonia
| NCBI | Quality Control | Links |
|---|---|---|
| Ornithinimicrobium |
Revision editor(s): Fortunehechi, Folakunmi
