Nasopharyngeal Microbiome Signature in COVID-19 Positive Patients: Can We Definitively Get a Role to Fusobacterium periodonticum?/Experiment 1
Curated date: 2021/06/28
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Peace Sandy
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
- Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx
- 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-19 negative controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 positive patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Symptomatic COVID-19 positive patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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
- Kruskall-Wallis
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3A-F
Description: Nasopaheryngeal microbiome composition in COVID-19 patients and Control group. The graphs show the percentage of relative abundance (%) of the all taxonomic levels from Phylum to Species, obtained by using the MicrobAT Suite - SmartSeq. Each column in the plot represents a group, and each color in the column represents the relative abundance (%) for each taxon. In panel (A) we show the phyla with average relative abundance greater than 1% in all studied groups; we found two phyla significantly less abundant in COVID-19 patients respect to Controls, Proteobacteria, and Fusobacteria. Not statistically significant difference in taxa abundance was observed when T0 and T1 COVID-19 patients were compared. The other panels (B–F) show the taxa abundance from class to up species level significantly different between groups by Kruskal Wallis test. (B) class (C) order, (D) family, (E) genus (F) species. *p < 0.05; **p < 0.001.
Abundance in Group 1: decreased abundance in COVID-19 positive patients
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacteriales | ||
| Fusobacteriota | ||
| Fusobacterium | ||
| Gammaproteobacteria | ||
| Haemophilus | ||
| Leptotrichia | ||
| Leptotrichiaceae | ||
| Pasteurellaceae | ||
| Pasteurellales |
Revision editor(s): Claregrieve1, Peace Sandy
