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

Study information

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

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

33815323

DOI Digital object identifier for electronic documents.

10.3389/fmicb.2021.637430

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

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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

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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 Control	Links
Alloprevotella
Catonella
Lachnoanaerobaculum
Oribacterium
Prevotella
unclassified Erysipelotrichaceae

Revision editor(s): Fatima, Claregrieve1

Experiment 2

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

Curated date: 2021/06/29

Curator: Claregrieve1

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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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: Not specified

Signature 1

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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 Control	Links
Treponema

Revision editor(s): Claregrieve1

Signature 2

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

Curated date: 2021/06/29

Curator: Claregrieve1

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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 Control	Links
uncultured phototrophic eukaryote

Revision editor(s): Claregrieve1

Experiment 3

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

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

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