Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection

Study information

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

36869345

DOI Digital object identifier for electronic documents.

https://doi.org/10.1186/s40168-022-01447-0

URI

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0

Authors

Li J, Jing Q, Li J, Hua M, Di L, Song C, Huang Y, Wang J, Chen C, Wu AR

Journal

Microbiome

Year

2023

Keywords:

COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract

BACKGROUND: The human microbiome plays an important role in modulating the host metabolism and immune system. Connections and interactions have been found between the microbiome of the gut and oral pharynx in the context of SARS-CoV-2 and other viral infections; hence, to broaden our understanding of host-viral responses in general and to deepen our knowledge of COVID-19, we performed a large-scale, systematic evaluation of the effect of SARS-CoV-2 infection on human microbiota in patients with varying disease severity. RESULTS: We processed 521 samples from 203 COVID-19 patients with varying disease severity and 94 samples from 31 healthy donors, consisting of 213 pharyngeal swabs, 250 sputa, and 152 fecal samples, and obtained meta-transcriptomes as well as SARS-CoV-2 sequences from each sample. Detailed assessment of these samples revealed altered microbial composition and function in the upper respiratory tract (URT) and gut of COVID-19 patients, and these changes are significantly associated with disease severity. Moreover, URT and gut microbiota show different patterns of alteration, where gut microbiome seems to be more variable and in direct correlation with viral load; and microbial community in the upper respiratory tract renders a high risk of antibiotic resistance. Longitudinally, the microbial composition remains relatively stable during the study period. CONCLUSIONS: Our study has revealed different trends and the relative sensitivity of microbiome in different body sites to SARS-CoV-2 infection. Furthermore, while the use of antibiotics is often essential for the prevention and treatment of secondary infections, our results indicate a need to evaluate potential antibiotic resistance in the management of COVID-19 patients in the ongoing pandemic. Moreover, a longitudinal follow-up to monitor the restoration of the microbiome could enhance our understanding of the long-term effects of COVID-19. Video Abstract.

Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2023/10/24

Curator: MyleeeA

Revision editor(s): MyleeeA, LGeistlinger

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

samples from Healthy patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Pharyngeal samples from COVID-19 patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria.

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

39

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

174

Lab analysis

Sequencing type

PCR

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)?

Yes

Alpha Diversity

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

decreased

Richness Number of species

unchanged

Signature 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2023/10/27

Curator: MyleeeA

Revision editor(s): MyleeeA, Folakunmi

Source: Within Results text ("Alteration of microbial composition in COVID-19 patients is associated with disease severity", lines 1-4)

Description: Altered microbial composition associated with disease severity

Abundance in Group 1: decreased abundance in Pharyngeal samples from COVID-19 patients

NCBI	Quality Control	Links
Burkholderia
Campylobacter
Escherichia
Fusobacterium
Haemophilus
Micrococcus
Neisseria
Selenomonas
Tannerella
Treponema

Revision editor(s): MyleeeA, Folakunmi

Signature 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2023/10/27

Curator: MyleeeA

Revision editor(s): MyleeeA, Folakunmi

Source: Within Results text ("Alteration of microbial composition in COVID-19 patients is associated with disease severity", lines 1-4)

Description: Altered microbial composition associated with disease severity

Abundance in Group 1: increased abundance in Pharyngeal samples from COVID-19 patients

NCBI	Quality Control	Links
Actinomyces
Rothia
Streptococcus

Revision editor(s): MyleeeA, Folakunmi

Experiment 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2023/10/27

Curator: MyleeeA

Revision editor(s): MyleeeA, LGeistlinger

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Sputum Expectoration,Sputum,sputum

Group 1 name Corresponds to the case (exposed) group for case-control studies

Sputum samples from COVID-19 patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria

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

15

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

235

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

Not Specified

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

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Your review change was submitted

Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2023/10/27

Curator: MyleeeA

Revision editor(s): MyleeeA, Folakunmi

Source: Within Results text ("Alteration of microbial composition in COVID-19 patients is associated with disease severity", lines 5-7)

Description: Altered microbial composition associated with disease severity

Abundance in Group 1: increased abundance in Sputum samples from COVID-19 patients

NCBI	Quality Control	Links
Capnocytophaga
Streptococcus

Revision editor(s): MyleeeA, Folakunmi

Signature 2

EditHistoryDelete

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2023/10/27

Curator: MyleeeA

Revision editor(s): MyleeeA, Folakunmi

Source: Within Results text ("Alteration of microbial composition in COVID-19 patients is associated with disease severity", lines 5-7)

Description: Altered microbial composition associated with disease severity

Abundance in Group 1: decreased abundance in Sputum samples from COVID-19 patients

NCBI	Quality Control	Links
Delftia
Haemophilus
Neisseria
Porphyromonas
Tannerella
Treponema

Revision editor(s): MyleeeA, Folakunmi

Experiment 3

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2023/10/27

Curator: MyleeeA

Revision editor(s): MyleeeA, LGeistlinger, Folakunmi

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Group 1 name Corresponds to the case (exposed) group for case-control studies

Feces samples from COVID-19 patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria.

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

40

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

112

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

N/A

Lab analysis

Statistical Analysis

Alpha Diversity

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

unchanged

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2023/10/27

Curator: MyleeeA

Revision editor(s): MyleeeA, Folakunmi

Source: Within Results text ("Alteration of microbial composition in COVID-19 patients is associated with disease severity", lines 13-16) Description: Altered microbial composition associated with disease severity

Description: Altered microbial composition associated with disease severity

Abundance in Group 1: increased abundance in Feces samples from COVID-19 patients

NCBI	Quality Control	Links
Halomonas
Pseudomonas

Revision editor(s): MyleeeA, Folakunmi

Signature 2

EditHistoryDelete

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2023/10/27

Curator: MyleeeA

Revision editor(s): MyleeeA, Folakunmi

Source: Within Results text ("Alteration of microbial composition in COVID-19 patients is associated with disease severity", lines 13-16)

Description: Altered microbial composition associated with disease severity.

Abundance in Group 1: decreased abundance in Feces samples from COVID-19 patients

NCBI	Quality Control	Links
Anaerostipes
Bifidobacterium
Eggerthella
Enterocloster
Faecalibacterium
Flavonifractor
Lachnoclostridium
Lachnospira
Parabacteroides
Roseburia

Revision editor(s): MyleeeA, Folakunmi