Association between the nasopharyngeal microbiome and metabolome in patients with COVID-19

Study information

Reviewed Marked as Reviewed by Fatima on 2022/05/11

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

34151035

DOI Digital object identifier for electronic documents.

10.1016/j.synbio.2021.06.002

URI

Authors

Liu J, Liu S, Zhang Z, Lee X, Wu W, Huang Z, Lei Z, Xu W, Chen D, Wu X, Guo Y, Peng L, Lin B, Chong Y, Mou X, Shi M, Lan P, Chen T, Zhao W, Gao Z

Journal

Synthetic and systems biotechnology

Year

2021

Keywords:

COVID-19, Metabolome, Nasopharyngeal microbiome, SARS-CoV-2, Susceptibility

SARS-CoV-2, the causative agent for COVID-19, infect human mainly via respiratory tract, which is heavily inhabited by local microbiota. However, the interaction between SARS-CoV-2 and nasopharyngeal microbiota, and the association with metabolome has not been well characterized. Here, metabolomic analysis of blood, urine, and nasopharyngeal swabs from a group of COVID-19 and non-COVID-19 patients, and metagenomic analysis of pharyngeal samples were used to identify the key features of COVID-19. Results showed lactic acid, l-proline, and chlorogenic acid methyl ester (CME) were significantly reduced in the sera of COVID-19 patients compared with non-COVID-19 ones. Nasopharyngeal commensal bacteria including Gemella morbillorum, Gemella haemolysans and Leptotrichia hofstadii were notably depleted in the pharynges of COVID-19 patients, while Prevotella histicola, Streptococcus sanguinis, and Veillonella dispar were relatively increased. The abundance of G. haemolysans and L. hofstadii were significantly positively associated with serum CME, which might be an anti-SARS-CoV-2 bacterial metabolite. This study provides important information to explore the linkage between nasopharyngeal microbiota and disease susceptibility. The findings were based on a very limited number of patients enrolled in this study; a larger size of cohort will be appreciated for further investigation.

Experiment 1

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Reviewed Marked as Reviewed by Fatima on 2022/05/11

Curated date: 2021/06/25

Curator: Claregrieve1

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

Subjects

Location of subjects: China

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: Non-COVID-19 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: Positive for infection with SARS-CoV-2 by nucleic acid testing

Group 0 sample size Number of subjects in the control (unexposed) group: 3

Group 1 sample size Number of subjects in the case (exposed) group: 6

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

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)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 3

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

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Reviewed Marked as Reviewed by Fatima on 2022/05/11

Curated date: 2021/06/25

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figures 3c-d

Description: Differential microbial abundance in nasopharyngeal samples between COVID-19 cases and controls

Abundance in Group 1: decreased abundance in COVID-19 patients

NCBI	Quality Control	Links
Gemella haemolysans
Campylobacter gracilis
Leptotrichia hofstadii
Gemella morbillorum
Stenotrophomonas maltophilia

Revision editor(s): Claregrieve1