Altered infective competence of the human gut microbiome in COVID-19.
COVID-19
Gut microbiome
Metagenomics
Metatranscriptomics
SARS-CoV-2
Journal
Microbiome
ISSN: 2049-2618
Titre abrégé: Microbiome
Pays: England
ID NLM: 101615147
Informations de publication
Date de publication:
09 03 2023
09 03 2023
Historique:
received:
31
10
2022
accepted:
24
01
2023
entrez:
9
3
2023
pubmed:
10
3
2023
medline:
14
3
2023
Statut:
epublish
Résumé
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. 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. Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.
Sections du résumé
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.
Identifiants
pubmed: 36894986
doi: 10.1186/s40168-023-01472-7
pii: 10.1186/s40168-023-01472-7
pmc: PMC9995755
doi:
Types de publication
Video-Audio Media
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
46Investigateurs
Geeta Acharya
(G)
Gloria Aguayo
(G)
Wim Ammerlaan
(W)
Ariane Assele-Kama
(A)
Christelle Bahlawane
(C)
Katy Beaumont
(K)
Nadia Beaupain
(N)
Lucrèce Beckers
(L)
Camille Bellora
(C)
Fay Betsou
(F)
Sandie Boly
(S)
Dirk Brenner
(D)
Eleftheria Charalambous
(E)
Emilie Charpentier
(E)
Manuel Counson
(M)
Brian De Witt
(B)
Olivia Domingues
(O)
Claire Dording
(C)
Bianca Dragomir
(B)
Tessy Fautsch
(T)
Jean-Yves Ferrand
(JY)
Ana Festas Lopes
(AF)
Joëlle Véronique Fritz
(JV)
Manon Gantenbein
(M)
Laura Georges
(L)
Jérôme Graas
(J)
Gael Hamot
(G)
Anne-Marie Hanff
(AM)
Maxime Hansen
(M)
Lisa Hefele
(L)
Estelle Henry
(E)
Margaux Henry
(M)
Eve Herkenne
(E)
Christiane Hilger
(C)
Judith Hübschen
(J)
Laetitia Huiart
(L)
Alexander Hundt
(A)
Gilles Iserentant
(G)
Stéphanie Kler
(S)
Pauline Lambert
(P)
Sabine Lehmann
(S)
Morgane Lemaire
(M)
Andrew Lumley
(A)
Monica Marchese
(M)
Sophie Mériaux
(S)
Maura Minelli
(M)
Alessandra Mousel
(A)
Maeva Munsch
(M)
Mareike Neumann
(M)
Magali Perquin
(M)
Achilleas Pexaras
(A)
Jean-Marc Plesseria
(JM)
Lucie Remark
(L)
Bruno Santos
(B)
Aurélie Sausy
(A)
Margaux Schmitt
(M)
Sneeha Seal
(S)
Jean-Yves Servais
(JY)
Florian Simon
(F)
Chantal Snoeck
(C)
Kate Sokolowska
(K)
Hermann Thien
(H)
Johanna Trouet
(J)
Jonathan Turner
(J)
Michel Vaillant
(M)
Daniela Valoura Esteves
(DV)
Charlène Verschueren
(C)
Tania Zamboni
(T)
Pinar Alper
(P)
Piotr Gawron
(P)
Enrico Glaab
(E)
Clarissa Gomes
(C)
Borja Gomez Ramos
(BG)
Vyron Gorgogietas
(V)
Valentin Groues
(V)
Wei Gu
(W)
Laurent Heirendt
(L)
Ahmed Hemedan
(A)
Sascha Herzinger
(S)
Anne Kaysen
(A)
Jacek Jaroslaw Lebioda
(JJ)
Tainà Marques
(T)
François Massart
(F)
Christiane Olesky
(C)
Venkata P Satagopam
(VP)
Claire Pauly
(C)
Laure Pauly
(L)
Lukas Pavelka
(L)
Guilherme Ramos Meyers
(GR)
Armin Rauschenberger
(A)
Basile Rommes
(B)
Kirsten Rump
(K)
Reinhard Schneider
(R)
Valerie Schröder
(V)
Amna Skrozic
(A)
Lara Stute
(L)
Noua Toukourou
(N)
Christophe Trefois
(C)
Carlos Vega Moreno
(CV)
Maharshi Vyas
(M)
Xinhui Wang
(X)
Anja Leist
(A)
Annika Lutz
(A)
Claus Vögele
(C)
Linda Hansen
(L)
João Manuel Loureiro
(JM)
Beatrice Nicolai
(B)
Alexandra Schweicher
(A)
Femke Wauters
(F)
Tamir Abdelrahman
(T)
Estelle Coibion
(E)
Guillaume Fournier
(G)
Marie Leick
(M)
Friedrich Mühlschlegel
(F)
Marie France Pirard
(MF)
Nguyen Trung
(N)
Philipp Jägi
(P)
Henry-Michel Cauchie
(HM)
Delphine Collart
(D)
Leslie Ogorzaly
(L)
Christian Penny
(C)
Cécile Walczak
(C)
Informations de copyright
© 2023. The Author(s).
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