Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Nath S, Sarkar M, Maddheshiya A, De D, Paul S, Dey S, Pal K, Roy SK, Ghosh A, Sengupta S, Paine SK, Biswas NK, Basu A, Mukherjee S
Journal
Microbiology spectrum
Year
2023
Keywords:
COVID-19, Delta, Omicron, URT, microbiome, next generation sequencing
The role of the upper respiratory tract (URT) microbiome in predicting lung health has been documented in several studies. The dysbiosis in COVID patients has been associated with disease outcomes by modulating the host immune system. However, although it has been known that different SARS-CoV-2 variants manifest distinct transmissibility and mortality rates in human populations, their effect on the composition and diversity of the URT microbiome has not been studied to date. Unlike the older variant (Delta), the newer variant (Omicron) have become more transmissible with lesser mortality and the symptoms have also changed significantly. Hence, in the present study, we have investigated the change in the URT microbiome associated with Delta and Omicron variants and identified variant-specific signatures that will be useful in the assessment of lung health and can be utilized for nasal probiotic therapy in the future.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-3-29
Subjects
- Location of subjects
- India
- 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
- Upper respiratory tract Upper respiratory tract,upper respiratory tract
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- SARS-CoV-2-related disease COVID-19-related disease,SARS-CoV-2-related disease,sARS-CoV-2-related disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients infected with COVID-19 virus (Delta and Omicron)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
Source: FIG 2
Description: LEfSe analysis of core species of COVID-19 patients and healthy controls.
Abundance in Group 1: increased abundance in COVID-19 patients
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
Source: FIG 2
Description: Relative abundances of bacteria in upper respiratory tract (URT) of Covid-19 patients and healthy group
Abundance in Group 1: decreased abundance in COVID-19 patients
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-3-29
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Delta and Omicron-infected patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients infected with the Delta and Omicron variants of SARS-CoV-2
Lab analysis
Statistical Analysis
- Statistical test
- ANOVA
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-3-29
Source: FIG 6
Description: Taxonomic difference among healthy controls, Delta-, and Omicron-infected patients.
Abundance in Group 1: decreased abundance in Delta and Omicron-infected patients
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae | ||
| Neisseria perflava | ||
| Fusobacterium pseudoperiodonticum | ||
| Neisseria subflava | ||
| Veillonella rogosae | ||
| Veillonella nakazawae |
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-3-29
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Omicron-infected patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Delta-infected patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients infected with Delta virus
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
Source: FIG 5
Description: Upper respiratory tract (URT) microbiome composition between Delta and Omicron infected patients.
Abundance in Group 1: increased abundance in Delta-infected patients
Revision editor(s): ModinatG
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
Source: FIG 5
Description: Upper respiratory tract (URT) microbiome composition between Delta and Omicron infected patients.
Abundance in Group 1: decreased abundance in Delta-infected patients
Revision editor(s): ModinatG
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