Altered infective competence of the human gut microbiome in COVID-19
Laura de Nies, Valentina Galata, Camille Martin‐Gallausiaux, Milena Despotović, Susheel Bhanu Busi, Chantal J. Snoeck, Léa Delacour, Deepthi Poornima Budagavi, Cédric C. Laczny, Janine Habier, Paula-Cristina Lupu, Rashi Halder, Joëlle V. Fritz, Tainá M. Marques, Estelle Sandt, Marc Paul O’Sullivan, Soumyabrata Ghosh, Venkata Satagopam, Geeta Acharya, Gloria Aguayo, Wim Ammerlaan, Ariane Assélé-Kama, Christelle Bahlawane, Katy Beaumont, Nadia Beaupain, Lucrèce Beckers, Camille Bellora, Fay Betsou, Sandie Boly, Dirk Brenner, Eleftheria Charalambous, Émilie Charpentier, Manuel Counson, Brian De Witt, Olivia Domingues, Claire Dording, Bianca Dragomir, Tessy Fautsch, Jean-Yves Ferrand, Ana Festas Lopes, Joëlle V. Fritz, Manon Gantenbein, Laura Georges, Jérôme Graas, Gaël Hamot, Anne-Marie Hanff, Maxime Hansen, Lisa Hefele, Estelle Henry, Margaux Henry, Eve Herkenne, Christiane Hilger, Judith M. Hübschen, Laëtitia Huiart, Alexander Hundt, Gilles Iserentant, Stéphanie Kler, Pauline Lambert, Sabine Lehmann, Morgane Lemaire, Andrew I. Lumley, Monica Marchese, Sophie B. Mériaux, Maura Minelli, Alessandra Mousel, Maeva Munsch, Mareike Neumann, Magali Perquin, Achilleas Pexaras, Jean‐Marc Plesséria, Lucie Remark, Bruno Santos, Aurélie Sausy, Margaux Schmitt, Sneeha Seal, Jean-Yves Servais, Florian Simon, Chantal J. Snoeck, Kate Sokolowska, Hermann Thien, Johanna Trouet, Jonathan D. Turner, Michel Vaillant, Daniela Esteves, Charlène Verschueren, Tania Zamboni, Pinar Alper, Piotr Gawron, Enrico Glaab, Clarissa P. C. Gomes, Borja Gomez Ramos, Vyron Gorgogietas, Valentin Grouès, Wei Gu, Laurent Heirendt, Ahmed Abdelmonem Hemedan, Sascha Herzinger, Anne Kaysen, Jacek Jaroslaw Lebioda, Tainá M. Marques
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.