Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-12

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

34425246

DOI Digital object identifier for electronic documents.

10.1016/j.micinf.2021.104880

URI

Authors

Gupta A, Karyakarte R, Joshi S, Das R, Jani K, Shouche Y, Sharma A

Journal

Microbes and infection

Year

2021

Keywords:

SARS-CoV-2, asymptomatic, host types, nasopharyngeal microbiome, symptomatic

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is causing a severe global health emergency owing to its highly infectious nature. Although the symptoms of SARS-CoV-2 are well known but its impact on nasopharyngeal microbiome is poorly studied. The present cross-sectional study was intended to understand the perturbation in the nasopharyngeal microbiome composition within the infected (n=63) and non-infected (n=26) individuals using 16S rRNA gene based targeted amplicon sequencing and their association with host types and the prevalence of opportunistic pathogens at the stage of infection. The results confirmed that number of OTUs were significantly (p < 0.05) decreased in the SARS-CoV-2 infected individuals in comparison to non-infected individuals. Pairwise Wilcoxon test showed a significant (p<0.05) increase in the abundance of Proteobacteria in infected individuals compared to non-infected ones and vice-versa for Fusobacteria and Bacteroidetes. Similarity percentage (SIMPER) analysis showed the increment in the abundance of opportunistic pathogens (Haemophilus, Stenotrophomonas, Acineobacter, Moraxella, Corynebacterium I, Gemella, Ralstonia, and Pseudomonas) involved in secondary infection. Furthermore, this study highlighted the microbial community structure of individuals within and across the families. Further, we also assessed the microbiome associated with host types (age and genders) and COVID-19 conditions (symptomatic and asymptomatic). The data suggested that the host types/conditions during the COVID-19 infection are potential factors in enrichment of specific bacterial communities in upper respiratory tract.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-12

Curated date: 2021/09/27

Curator: Claregrieve1

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

Subjects

Location of subjects: India

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-infected controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: COVID-19 cases

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: COVID-19 infected individuals

Group 0 sample size Number of subjects in the control (unexposed) group: 26

Group 1 sample size Number of subjects in the case (exposed) group: 63

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: 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: Mann-Whitney (Wilcoxon)

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

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

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

Richness Number of species: decreased

Signature 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-12

Curated date: 2021/09/27

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Supplementary Info - Figure 1

Description: Differential abundance of microbial taxa between infected and non-infected individuals

Abundance in Group 1: increased abundance in COVID-19 cases

NCBI	Quality Control	Links
Pseudomonadota

Revision editor(s): Claregrieve1

Signature 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-12

Curated date: 2021/09/27

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Peace Sandy

Source: Supplementary Info - Figure 1, Figure 2a-b

Description: Differential abundance of microbial taxa between infected and non-infected individuals

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

NCBI	Quality Control	Links
Bacillota
Bacteroidota
Fusobacteriaceae
Fusobacterium
Haemophilus
Leptotrichiaceae
Neisseria
Neisseriaceae
Prevotellaceae
Streptococcus
Veillonellaceae
Prevotella
Porphyromonadaceae

Revision editor(s): Claregrieve1, Peace Sandy