Altered infective competence of the human gut microbiome in COVID-19
Authors: de Nies Laura , Galata Valentina , Martin-Gallausiaux Camille , Despotovic Milena , Busi Susheel Bhanu , Snoeck Chantal J. , Delacour Lea , Budagavi Deepthi Poornima , Laczny Cédric Christian , Habier Janine , Lupu Paula-Cristina , Halder Rashi , Fritz Joëlle V. , Marques Taina , Sandt Estelle , O’Sullivan Marc Paul , Ghosh Soumyabrata , Satagopam Venkata ,   CON-VINCE Consortium, Acharya Geeta , Aguayo Gloria , Ammerlaan Wim , Assele-Kama Ariane , Bahlawane Christelle , Beaumont Katy , Beaupain Nadia , Beckers Lucrèce , Bellora Camille , Betsou Fay , Boly Sandie , Brenner Dirk , Charalambous Eleftheria , Charpentier Emilie , Counson Manuel , De Witt Brian , Domingues Olivia , Dording Claire , Dragomir Bianca , Fautsch Tessy , Ferrand Jean-Yves , Lopes Ana Festas , Fritz Joëlle Véronique , Gantenbein Manon , Georges Laura , Graas Jérôme , Hamot Gael , Hanff Anne-Marie , Hansen Maxime , Hefele Lisa , Henry Estelle , Henry Margaux , Herkenne Eve , Hilger Christiane , Hübschen Judith , Huiart Laetitia , Hundt Alexander , Iserentant Gilles , Kler Stéphanie , Lambert Pauline , Lehmann Sabine , Lemaire Morgane , Lumley Andrew , Marchese Monica , Mériaux Sophie , Minelli Maura , Mousel Alessandra , Munsch Maeva , Neumann Mareike , Perquin Magali , Pexaras Achilleas , Plesseria Jean-Marc , Remark Lucie , Santos Bruno , Sausy Aurélie , Schmitt Margaux , Seal Sneeha , Servais Jean-Yves , Simon Florian , Snoeck Chantal , Sokolowska Kate , Thien Hermann , Trouet Johanna , Turner Jonathan , Vaillant Michel , Esteves Daniela Valoura , Verschueren Charlène , Zamboni Tania , Alper Pinar , Gawron Piotr , Glaab Enrico , Gomes Clarissa , Ramos Borja Gomez , Gorgogietas Vyron , Groues Valentin , Gu Wei , Heirendt Laurent , Hemedan Ahmed , Herzinger Sascha , Kaysen Anne , Lebioda Jacek Jaroslaw , Marques Tainà , Massart François , Olesky Christiane , Satagopam Venkata P. , Pauly Claire , Pauly Laure , Pavelka Lukas , Meyers Guilherme Ramos , Rauschenberger Armin , Rommes Basile , Rump Kirsten , Schneider Reinhard , Schröder Valerie , Skrozic Amna , Stute Lara , Toukourou Noua , Trefois Christophe , Moreno Carlos Vega , Vyas Maharshi , Wang Xinhui , Leist Anja , Lutz Annika , Vögele Claus , Hansen Linda , Loureiro João Manuel , Nicolai Beatrice , Schweicher Alexandra , Wauters Femke , Abdelrahman Tamir , Coibion Estelle , Fournier Guillaume , Leick Marie , Mühlschlegel Friedrich , Pirard Marie France , Trung Nguyen , Jägi Philipp , Cauchie Henry-Michel , Collart Delphine , Ogorzaly Leslie , Penny Christian , Walczak Cécile , Krüger Rejko , Fagherazzi Guy , Ollert Markus , Hefeng Feng Q. , May Patrick , Wilmes Paul 
Published: March 2023

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.