Altered infective competence of the human gut microbiome in COVID-19

Study information

Reviewed Marked as Reviewed by Fatima on 2023-4-13

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

36894986

DOI Digital object identifier for electronic documents.

https://doi.org/10.1186/s40168-023-01472-7

URI

Authors

de Nies L, Galata V, Martin-Gallausiaux C, Despotovic M, Busi SB, Snoeck CJ, Delacour L, Budagavi DP, Laczny CC, Habier J, Lupu PC, Halder R, Fritz JV, Marques T, Sandt E, O'Sullivan MP, Ghosh S, Satagopam V, Krüger R, Fagherazzi G, Ollert M, Hefeng FQ, May P, Wilmes P

Journal

Microbiome

Year

2023

Keywords:

COVID-19, Gut microbiome, Metagenomics, Metatranscriptomics, SARS-CoV-2

BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group. RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls. CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.

Experiment 1

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Reviewed Marked as Reviewed by Fatima on 2023-4-13

Curated date: 2023/03/11

Curator: Busayo

Revision editor(s): Busayo, Atrayees, Fatima

Subjects

Location of subjects: United States of America

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: 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

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: Control group

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: These individuals had confirmed SARS-CoV-2 infection by a positive RT-PCR test result and presented with COVID-19 symptoms such as fever, cough, and difficulty breathing.

Group 0 sample size Number of subjects in the control (unexposed) group: 57

Group 1 sample size Number of subjects in the case (exposed) group: 61

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months

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: Mann-Whitney (Wilcoxon)

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: 2.0

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

Alpha Diversity

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

Signature 1

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Reviewed Marked as Reviewed by Fatima on 2023-4-13

Curated date: 2023/03/11

Curator: Busayo

Revision editor(s): Busayo, Fatima

Source: Figure 2B

Description: Relative abundance of bacterial species significantly enriched in COVID-19 patients compared to the control group

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

NCBI	Quality Control	Links
Firmicutes bacterium AM10-47
Prevotella sp. CAG:520
Roseburia sp. CAG:471
Leyella stercorea

Revision editor(s): Busayo, Fatima

Signature 2

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Reviewed Marked as Reviewed by Fatima on 2023-4-13

Curated date: 2023/03/11

Curator: Busayo

Revision editor(s): Busayo

Source: Figure 2C

Description: Relative abundance of bacterial species significantly decreased in COVID-19 patients compared to the control group

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

NCBI	Quality Control	Links
Firmicutes bacterium CAG:145
Roseburia faecis
Turicibacter sanguinis

Revision editor(s): Busayo