Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 +

Study information

Reviewed Marked as Reviewed by Folakunmi on 2024-2-19

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

37803040

DOI Digital object identifier for electronic documents.

10.1038/s41598-023-43040-x

URI

Authors

Bellato M, Cappellato M, Longhin F, Del Vecchio C, Brancaccio G, Cattelan AM, Brun P, Salaris C, Castagliuolo I, Di Camillo B

Journal

Scientific reports

Year

2023

The outbreak of Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, forced us to face a pandemic with unprecedented social, economic, and public health consequences. Several nations have launched campaigns to immunize millions of people using various vaccines to prevent infections. Meanwhile, therapeutic approaches and discoveries continuously arise; however, identifying infected patients that are going to experience the more severe outcomes of COVID-19 is still a major need, to focus therapeutic efforts, reducing hospitalization and mitigating drug adverse effects. Microbial communities colonizing the respiratory tract exert significant effects on host immune responses, influencing the susceptibility to infectious agents. Through 16S rDNAseq we characterized the upper airways' microbiota of 192 subjects with nasopharyngeal swab positive for SARS-CoV-2. Patients were divided into groups based on the presence of symptoms, pneumonia severity, and need for oxygen therapy or intubation. Indeed, unlike most of the literature, our study focuses on identifying microbial signatures predictive of disease progression rather than on the probability of infection itself, for which a consensus is lacking. Diversity, differential abundance, and network analysis at different taxonomic levels were synergistically adopted, in a robust bioinformatic pipeline, highlighting novel possible taxa correlated with patients' disease progression to intubation.

Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2023/10/17

Curator: Fortunehechi

Revision editor(s): LGeistlinger, Peace Sandy, Folakunmi, Fortunehechi

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 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: Asymptomatic patients

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Symptomatic patients with signs of COVID-19

Group 0 sample size Number of subjects in the control (unexposed) group: 36

Group 1 sample size Number of subjects in the case (exposed) group: 156

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Patients were excluded from the study if they had received antibiotics within 4 weeks of enrollment.

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

Experiment 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2023/10/23

Curator: Fortunehechi

Revision editor(s): Fortunehechi, LGeistlinger, Folakunmi

Differences from previous experiment shown

Subjects

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

Statistical Analysis

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

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2023/10/24

Curator: Fortunehechi

Revision editor(s): Fortunehechi, Folakunmi

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

Experiment 3

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2023/11/13

Curator: Fortunehechi

Revision editor(s): LGeistlinger, Fortunehechi, Folakunmi

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: COVID-19 , Respiratory failure requiring assisted ventilation 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,Respiratory distress necessitating mechanical ventilation,Respiratory distress requiring endotracheal intubation,Respiratory distress requiring mechanical ventilation,Respiratory failure requiring assisted ventilation,respiratory failure requiring assisted ventilation

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients unable to provide enough oxygen to their body.

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

Group 1 sample size Number of subjects in the case (exposed) group: 18

Lab analysis

Statistical Analysis

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

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Curated date: 2024/02/17

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Source: Table 3

Description: MaAsLin2 differentially abundant taxa analysis in COVID patients with and without intubation

Abundance in Group 1: increased abundance in Intubated

NCBI	Quality Control	Links
Jonquetella anthropi
Ornithinimicrobium pekingense
unclassified Enterococcus
Ornithinimicrobium

Revision editor(s): Folakunmi

Experiment 4

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2023/11/13

Curator: Fortunehechi

Revision editor(s): Fortunehechi, Folakunmi

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Response to supplemental oxygen response to oxygen therapy,Response to supplemental oxygen,response to supplemental oxygen

Group 0 name Corresponds to the control (unexposed) group for case-control studies: No Supplemental O2

Group 1 name Corresponds to the case (exposed) group for case-control studies: Supplemental O2 (High/Low)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients in need of supply of oxygen to help them breathe better and keep their blood oxygen levels up.