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

Laura de Nies; Valentina Galata; Camille Martin-Gallausiaux; Milena Despotovic; Susheel Bhanu Busi; Chantal J. Snoeck; Lea Delacour; Deepthi Poornima Budagavi; Cédric Christian Laczny; Janine Habier; Paula Cristina Lupu; Rashi Halder; Joëlle V. Fritz; Taina Marques; Estelle Sandt; Marc Paul O'Sullivan; Soumyabrata Ghosh; Venkata Satagopam; Rejko Krüger; Guy Fagherazzi; Markus Ollert; Feng Q. Hefeng; Patrick May; Paul Wilmes; CON-VINCE Consortium; Margaux Henry; Ana Festas Lopes; Maeva Munsch; Lucie Remark; Florian Simon; Judith Hübschen

doi:10.1186/s40168-023-01472-7

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

Laura de Nies, Valentina Galata, Camille Martin-Gallausiaux, Milena Despotovic, Susheel Bhanu Busi, Chantal J. Snoeck, Lea Delacour, Deepthi Poornima Budagavi, Cédric Christian Laczny, Janine Habier, Paula Cristina Lupu, Rashi Halder, Joëlle V. Fritz, Taina Marques, Estelle Sandt, Marc Paul O'Sullivan, Soumyabrata Ghosh, Venkata Satagopam, Rejko Krüger, Guy FagherazziMarkus Ollert, Feng Q. Hefeng, Patrick May, Paul Wilmes^*, CON-VINCE Consortium, Margaux Henry, Ana Festas Lopes, Maeva Munsch, Lucie Remark, Florian Simon, Judith Hübschen

^*Corresponding author for this work

Research output: Contribution to journal › Article › Research › peer-review

14 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	46
Number of pages	1
Journal	Microbiome
Volume	11
Issue number	1
DOIs	https://doi.org/10.1186/s40168-023-01472-7
Publication status	Published - 9 Mar 2023

Keywords

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

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de Nies, L., Galata, V., Martin-Gallausiaux, C., Despotovic, M., Busi, S. B., Snoeck, C. J., Delacour, L., Budagavi, D. P., Laczny, C. C., Habier, J., Lupu, P. C., Halder, R., Fritz, J. V., Marques, T., Sandt, E., O'Sullivan, M. P., Ghosh, S., Satagopam, V., Krüger, R., ... Hübschen, J. (2023). Altered infective competence of the human gut microbiome in COVID-19. Microbiome, 11(1), 46. https://doi.org/10.1186/s40168-023-01472-7

@article{cb6a18abf94e4eb0baecddd6bf5879df,

title = "Altered infective competence of the human gut microbiome in COVID-19",

abstract = "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.",

keywords = "COVID-19, Gut microbiome, Metagenomics, Metatranscriptomics, SARS-CoV-2",

author = "{de Nies}, Laura and Valentina Galata and Camille Martin-Gallausiaux and Milena Despotovic and Busi, {Susheel Bhanu} and Snoeck, {Chantal J.} and Lea Delacour and Budagavi, {Deepthi Poornima} and Laczny, {C{\'e}dric Christian} and Janine Habier and Lupu, {Paula Cristina} and Rashi Halder and Fritz, {Jo{\"e}lle V.} and Taina Marques and Estelle Sandt and O'Sullivan, {Marc Paul} and Soumyabrata Ghosh and Venkata Satagopam and Rejko Kr{\"u}ger and Guy Fagherazzi and Markus Ollert and Hefeng, {Feng Q.} and Patrick May and Paul Wilmes and {CON-VINCE Consortium} and Margaux Henry and {Festas Lopes}, Ana and Maeva Munsch and Lucie Remark and Florian Simon and Judith H{\"u}bschen",

note = "Funding: The Predi COVID study is supported by the Luxembourg National Research Fund (FNR: 14716273), the Fondation Andr{\'e} Losch, and the European Regional Development Fund (FEDER, no. 2018–04 026–21). F.Q.H. was partially sup ported by FNR AFR RIKEN bilateral program (TregBAR, 11228353, F.Q.H. and M.O.) and PRIDE program (11012546/NEXTIMMUNE and 10907093/CRITICS). The CON VINCE study is supported by the Fonds National de la Recherche (FNR: 14716281/CON VINCE/Kruger) and the Andr{\'e} Losch Foundation. P.W. acknowledges funding from the European Research Council under the Euro pean Union{\textquoteright}s Horizon 2020 research and innovation program (no. 863664). LdN, PM, and PW are supported by the Luxembourg National Research Fund (FNR; PRIDE17/11823097) awarded to PW. We would also like to acknowl edge the following funding instruments: FNR: COVID 19/2020–1/14719552/ FunBiome. The work was further supported by the Luxembourg Government through the CoVaLux program. This research has also been supported by the Swiss National Science Foundation (CRSII5_180241) supporting SBB. {\textcopyright} 2023. The Author(s).",

year = "2023",

month = mar,

day = "9",

doi = "10.1186/s40168-023-01472-7",

language = "English",

volume = "11",

pages = "46",

journal = "Microbiome",

issn = "2049-2618",

publisher = "BioMed Central Ltd.",

number = "1",

}

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, CON-VINCE Consortium, Henry, M, Festas Lopes, A , Munsch, M , Remark, L, Simon, F & Hübschen, J 2023, 'Altered infective competence of the human gut microbiome in COVID-19', Microbiome, vol. 11, no. 1, pp. 46. https://doi.org/10.1186/s40168-023-01472-7

TY - JOUR

T1 - Altered infective competence of the human gut microbiome in COVID-19

AU - de Nies, Laura

AU - Galata, Valentina

AU - Martin-Gallausiaux, Camille

AU - Despotovic, Milena

AU - Busi, Susheel Bhanu

AU - Snoeck, Chantal J.

AU - Delacour, Lea

AU - Budagavi, Deepthi Poornima

AU - Laczny, Cédric Christian

AU - Habier, Janine

AU - Lupu, Paula Cristina

AU - Halder, Rashi

AU - Fritz, Joëlle V.

AU - Marques, Taina

AU - Sandt, Estelle

AU - O'Sullivan, Marc Paul

AU - Ghosh, Soumyabrata

AU - Satagopam, Venkata

AU - Krüger, Rejko

AU - Fagherazzi, Guy

AU - Ollert, Markus

AU - Hefeng, Feng Q.

AU - May, Patrick

AU - Wilmes, Paul

AU - CON-VINCE Consortium

AU - Henry, Margaux

AU - Festas Lopes, Ana

AU - Munsch, Maeva

AU - Remark, Lucie

AU - Simon, Florian

AU - Hübschen, Judith

N1 - Funding: The Predi COVID study is supported by the Luxembourg National Research Fund (FNR: 14716273), the Fondation André Losch, and the European Regional Development Fund (FEDER, no. 2018–04 026–21). F.Q.H. was partially sup ported by FNR AFR RIKEN bilateral program (TregBAR, 11228353, F.Q.H. and M.O.) and PRIDE program (11012546/NEXTIMMUNE and 10907093/CRITICS). The CON VINCE study is supported by the Fonds National de la Recherche (FNR: 14716281/CON VINCE/Kruger) and the André Losch Foundation. P.W. acknowledges funding from the European Research Council under the Euro pean Union’s Horizon 2020 research and innovation program (no. 863664). LdN, PM, and PW are supported by the Luxembourg National Research Fund (FNR; PRIDE17/11823097) awarded to PW. We would also like to acknowl edge the following funding instruments: FNR: COVID 19/2020–1/14719552/ FunBiome. The work was further supported by the Luxembourg Government through the CoVaLux program. This research has also been supported by the Swiss National Science Foundation (CRSII5_180241) supporting SBB. © 2023. The Author(s).

PY - 2023/3/9

Y1 - 2023/3/9

N2 - 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.

AB - 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.

KW - COVID-19

KW - Gut microbiome

KW - Metagenomics

KW - Metatranscriptomics

KW - SARS-CoV-2

UR - http://www.scopus.com/inward/record.url?scp=85149671201&partnerID=8YFLogxK

UR - https://pubmed.ncbi.nlm.nih.gov/36894986

U2 - 10.1186/s40168-023-01472-7

DO - 10.1186/s40168-023-01472-7

M3 - Article

C2 - 36894986

SN - 2049-2618

VL - 11

SP - 46

JO - Microbiome

JF - Microbiome

IS - 1

ER -

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

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Keywords

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