Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19

From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/04/20
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Ventero MP, Cuadrat RRC, Vidal I, Andrade BGN, Molina-Pardines C, Haro-Moreno JM, Coutinho FH, Merino E, Regitano LCA, Silveira CB, Afli H, López-Pérez M, Rodríguez JC
Journal
Frontiers in microbiology
Year
2021
Keywords:
COVID-19, NGS – next generation sequencing, Prevotella, SARS-CoV-2, coronavirus, microbiome
Background: SARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however, only one study so far focused on the patient's nasopharynx microbiota. In this study we investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19. We performed 16S ribosomal DNA sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization), and severe (admission to ICU). We compared the microbiota diversity and OTU composition among severity groups and built bacterial co-abundance networks for each group. Results: Statistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidota (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthermore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms. Conclusion: Our study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. Taxa with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results.

Experiment 1


Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Peace Sandy

Subjects

Location of subjects
Spain
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
Severe COVID-19 patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with confirmed COVID-19 infection and severe symptoms; required hospital admission
Group 0 sample size Number of subjects in the control (unexposed) group
18
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
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).
raw counts
Statistical test
Linear Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.25
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, sex


Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Fatima, Claregrieve1

Source: Supplemental Table S5

Description: Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients

Abundance in Group 1: increased abundance in Severe COVID-19 patients

NCBI Quality ControlLinks
Alloprevotella
Catonella
Lachnoanaerobaculum
Oribacterium
Prevotella
unclassified Erysipelotrichaceae

Revision editor(s): Fatima, Claregrieve1

Experiment 2


Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Severe COVID-19 patients requiring ICU
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with confirmed COVID-19 infection and severe symptoms who were admitted into the intensive care unit
Group 1 sample size Number of subjects in the case (exposed) group
19

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplemental Table S5

Description: Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients requiring ICU care

Abundance in Group 1: increased abundance in Severe COVID-19 patients requiring ICU

NCBI Quality ControlLinks
Treponema

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplemental Table S5

Description: Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients requiring ICU care

Abundance in Group 1: decreased abundance in Severe COVID-19 patients requiring ICU

NCBI Quality ControlLinks
uncultured phototrophic eukaryote

Revision editor(s): Claregrieve1

Experiment 3


Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Mild COVID-19 patients
Group 1 name Corresponds to the case (exposed) group for case-control studies
Severe COVID-19 patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with confirmed COVID-19 infection and severe symptoms who were hospitalized
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
18

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/20

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplemental Table S5

Description: Differential abundance of bacterial taxa between mild and severe COVID-19 cases

Abundance in Group 1: increased abundance in Severe COVID-19 patients

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Claregrieve1