Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients

Study information

Reviewed Marked as Reviewed by Svetlana up on 2024-8-15

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

37158877

DOI Digital object identifier for electronic documents.

10.1186/s12866-023-02872-3

URI

Authors

Wei N, Zhu G, Zhao T, Wang Y, Lou H, Li H, Yang Z, Zhang Z, Wang Q, Han M, Lin Z, Li S

Journal

BMC microbiology

Year

2023

Keywords:

COVID-19, Oral bacteria, Oral fungi, Recovered patients, Virus clearance

COVID-19 has emerged as a global pandemic, challenging the world's economic and health systems. Human oral microbiota comprises the second largest microbial community after the gut microbiota and is closely related to respiratory tract infections; however, oral microbiomes of patients who have recovered from COVID-19 have not yet been thoroughly studied. Herein, we compared the oral bacterial and fungal microbiota after clearance of SARS-CoV-2 in 23 COVID-19 recovered patients to those of 29 healthy individuals. Our results showed that both bacterial and fungal diversity were nearly normalized in recovered patients. The relative abundance of some specific bacteria and fungi, primarily opportunistic pathogens, decreased in recovered patients (RPs), while the abundance of butyrate-producing organisms increased in these patients. Moreover, these differences were still present for some organisms at 12 months after recovery, indicating the need for long-term monitoring of COVID-19 patients after virus clearance.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-8-15

Curated date: 2024/04/27

Curator: Junie

Revision editor(s): Junie, Victoria

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: Throat Gula,Throat,throat

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: HCs (Healthy Controls)

Group 1 name Corresponds to the case (exposed) group for case-control studies: RPs (Recovered Patients)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group consists of patients who have recovered from COVID-19.

Group 0 sample size Number of subjects in the control (unexposed) group: 29

Group 1 sample size Number of subjects in the case (exposed) group: 23

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 months

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).: 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)?: Yes

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-8-15

Curated date: 2024/08/09

Curator: Victoria

Revision editor(s): Victoria

Source: Fig. 3A & Fig. 6A

Description: Images showing the differences in taxa between RPs and HCs. (Fig. 3A shows oral bacterial taxa, while Fig. 6A shows oral fungi taxa).

Abundance in Group 1: increased abundance in RPs (Recovered Patients)

NCBI	Quality Control	Links
Arcobacter
Arcobacteraceae
Diaporthaceae
Diaporthales
Diaporthe
Lactobacillaceae
Paenibacillus
Sordariomycetes
Talaromyces
Thermaceae
Thermus
Weissella
Johnsonella
Oribacterium
Stomatobaculum
Lachnospiraceae
Bulleidia
Veillonella
Veillonellaceae
Fusobacterium
Fusobacteriaceae
Sneathia
uncultureduncultured
Aquamicrobium
Liberibacter
Ochrobactrum
Rhizobiaceae
Vogesella
Chromobacteriaceae
C39C39
Moraxella

Revision editor(s): Victoria

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-8-15

Curated date: 2024/08/10

Curator: Victoria

Revision editor(s): Victoria

Source: Fig. 3A & Fig. 6A

Description: Images showing the differences in taxa between RPs and HCs. (Fig. 3A shows oral bacterial taxa, while Fig. 6A shows oral fungi taxa).

Abundance in Group 1: decreased abundance in RPs (Recovered Patients)

NCBI	Quality Control	Links
Candida
Saccharomycetales fam incertae sedisSaccharomycetales fam incertae sedis
Arachnia
Propionibacteriaceae
Alloprevotella
Prevotella
Elizabethkingia
Empedobacter
Vagococcus
Clostridiaceae 1Clostridiaceae 1
Caulobacteraceae
Methylobacterium
Mesorhizobium
Bradyrhizobium
Xanthobacteraceae
Wolbachia
Anaplasmataceae
Candidatus Profftella
Lautropia
Ralstonia
Burkholderiaceae
Aggregatibacter
Vibrio
Vibrionaceae

Revision editor(s): Victoria