Article, 2023
Altered infective competence of the human gut microbiome in COVID-19
Microbiome,
ISSN
2049-2618,
Volume 11,
1,
10.1186/s40168-023-01472-7
Contributors
de Nies L.
[1]
Galata V.
[1]
Martin-Gallausiaux C.
[1]
Despotovic M.
[1]
Busi S.B.
[1]
Snoeck C.J.
0000-0002-0000-1850
[2]
Delacour L.
[1]
Budagavi D.P.
[1]
Laczny C.C.
[1]
Habier J.
[1]
Lupu P.-C.
[1]
Halder R.
0000-0002-1402-1254
[1]
Fritz J.V.
[2]
Marques T.
0000-0001-6098-2817
[1]
Sandt E.
[2]
O'Sullivan M.P.
[2]
Ghosh S.
[1]
Satagopam V.
0000-0002-6532-5880
[1]
Acharya G.
Aguayo G.A.
0000-0002-5625-1664
Ammerlaan W.
Assele-Kama A.
Bahlawane C.
Beaumont K.
Beaupain N.
Beckers L.
Bellora C.
Betsou F.
0000-0002-0558-4653
Boly S.
Brenner D.
0000-0001-8979-1045
Charalambous E.
Charpentier E.
Counson M.
De Witt B.
Domingues O.
Dording C.
Dragomir B.
Fautsch T.
Ferrand J.-Y.
Lopes A.F.
Fritz J.V.
Gantenbein M.
Georges L.
Graas J.
Hamot G.
Hanff A.-M.
Hansen M.
Hefele L.
Henry E.
Henry M.
Herkenne E.
Hilger C.
0000-0001-9455-5442
Hubschen J.M.
Huiart L.
0000-0002-5401-1958
Hundt A.
Iserentant G.
Kler S.
Lambert P.
Lehmann S.
Lemaire M.
Lumley A.
0000-0001-5935-3327
Marchese M.
Meriaux S.
Minelli M.
Mousel A.
Munsch M.
Neumann M.
Perquin M.
Pexaras A.
Plesseria J.-M.
Remark L.
Santos B.
0000-0002-8849-576X
Sausy A.
Schmitt M.
Seal S.
Servais J.-Y.
Simon F.
Snoeck C.J.
0000-0002-0000-1850
Sokolowska K.
Thien H.
Trouet J.
Turner J.D.
0000-0002-2760-1071
Vaillant M.
Esteves D.V.
Verschueren C.
Zamboni T.
Alper P.
Gawron P.
Glaab E.
Gomes C.
0000-0003-0269-6470
Ramos B.G.
Gorgogietas V.
Groues V.
Gu W.
Heirendt L.
Hemedan A.
Herzinger S.
Kaysen A.
Lebioda J.J.
Marques T.
0000-0001-6098-2817
Massart F.
Olesky C.
Satagopam V.
0000-0002-6532-5880
Pauly C.
Pauly L.
Pavelka L.
Meyers G.R.
Rauschenberger A.
Rommes B.
Rump K.
Schneider R.
0000-0002-8278-1618
Schroder V.
Skrozic A.
Stute L.
Toukourou N.
Trefois C.
Moreno C.V.
Vyas M.
Wang X.
Leist A.
Lutz A.
Vogele C.
Hansen L.
Loureiro J.M.
Nicolai B.
Schweicher A.
Wauters F.
Abdelrahman T.
Coibion E.
Fournier G.
Leick M.
Muhlschlegel F.
Pirard M.F.
Trung N.
Jagi P.
Cauchie H.-M.
Collart D.
Ogorzaly L.
Penny C.
Walczak C.
Kruger R.
[1]
[2]
Fagherazzi G.
0000-0001-5033-5966
[2]
Ollert M.
0000-0002-8055-0103
[2]
[3]
Hefeng F.Q.
0000-0003-2657-7361
[2]
May P.
0000-0001-8698-3770
[1]
Wilmes P.
0000-0002-6478-2924
(Corresponding author)
[1]
Affiliations
- [1]
University of Luxembourg
[NORA names:
Luxembourg; Europe, EU; OECD];
- [2]
Luxembourg Institute of Health
[NORA names:
Luxembourg; Europe, EU; OECD];
- [3]
Odense University Hospital
[NORA names:
Region of Southern Denmark; Hospital; Denmark; Europe, EU; Nordic; OECD]
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. [MediaObject not available: see fulltext.]
Keywords
COVID-19,
Gut microbiome,
Metagenomics,
Metatranscriptomics,
SARS-CoV-2
Funders
Data Provider: Elsevier