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

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


Needs review

Curated date: 2023/10/17

Curator: Fortunehechi

Revision editor(s): Fortunehechi, LGeistlinger

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
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
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).
centered log-ratio
Statistical test
Linear Regression
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

Needs review

Curated date: 2023/10/23

Curator: Fortunehechi

Revision editor(s): Fortunehechi

Source: Figure 1

Description: This signature represents the genus Subdoligranulum which is decreased in abundance in group 1

Abundance in Group 1: decreased abundance in Symptomatic patients

NCBI Quality ControlLinks
Subdoligranulum

Revision editor(s): Fortunehechi

Signature 2

Needs review

Curated date: 2023/10/23

Curator: Fortunehechi

Revision editor(s): Fortunehechi

Source: Figure 1

Description: This signature shows that the genus Clostridiales bacterium would be increased in abundance in group 1

Abundance in Group 1: increased abundance in Symptomatic patients

NCBI Quality ControlLinks
Clostridiales bacterium

Revision editor(s): Fortunehechi

Experiment 2


Needs review

Curated date: 2023/10/23

Curator: Fortunehechi

Revision editor(s): Fortunehechi, LGeistlinger

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,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)
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 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

Statistical test
ANOVA
Linear Regression
T-Test
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, comorbidity, sex

Alpha Diversity

Pielou Quantifies how equal the community is numerically
increased
Richness Number of species
decreased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
decreased

Signature 1

Needs review

Curated date: 2023/10/24

Curator: Fortunehechi

Revision editor(s): Fortunehechi

Source: Table 3

Description: This signature shows that there’s increased abundance in COVID

Abundance in Group 1: increased abundance in COVID-19 patients with severe pneumonia

NCBI Quality ControlLinks
Bacillus
Bifidobacterium
Enterococcus
Jonquetella
Moraxella
Ornithinimicrobium
Sphingopyxis
Staphylococcus
Phycicoccus sp.

Revision editor(s): Fortunehechi

Signature 2

Needs review

Curated date: 2023/10/24

Curator: Fortunehechi

Revision editor(s): Fortunehechi

Source: Table 3

Description: This signature shows or indicates the decrease in COVID-19

Abundance in Group 1: decreased abundance in COVID-19 patients with severe pneumonia

NCBI Quality ControlLinks
Actinomyces
Haemophilus
Oribacterium
Porphyromonas
Prevotella
Selenomonas
Thioclava
Chitinilyticum

Revision editor(s): Fortunehechi

Experiment 3


Needs review

Curated date: 2023/11/13

Curator: Fortunehechi

Revision editor(s): Fortunehechi, LGeistlinger

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,Respiratory distress necessitating mechanical ventilation,Respiratory distress requiring endotracheal intubation,Respiratory distress requiring mechanical 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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
Not specified

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 4


Needs review

Curated date: 2023/11/13

Curator: Fortunehechi

Revision editor(s): Fortunehechi

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
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
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.
Group 1 sample size Number of subjects in the case (exposed) group
72

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